moved to ../include/ZMap

src/zmapWindow/zmapcommon.h

-/*  Last edited: Jun  9 11:47 2004 (rnc) */
-/*  file: zmapcommon.h
- *  Author: Rob Clack (rnc@sanger.ac.uk)
- *  Copyright (c) Sanger Institute, 2003
- *-------------------------------------------------------------------
- * Zmap is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
- * or see the on-line version at http://www.gnu.org/copyleft/gpl.txt
- *-------------------------------------------------------------------
- * This file is part of the ZMap genome database package
- * and was written by
- *      Rob Clack (Sanger Institute, UK) rnc@sanger.ac.uk,
- * 	Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk and
- *	Simon Kelley (Sanger Institute, UK) srk@sanger.ac.uk
- *
- * zmapcommon.h holds definitions which are required both by xace and zmap.
- */
-
-#ifndef ZMAPCOMMON_H
-#define ZMAPCOMMON_H
-
-#include <../acedb/graph.h>
-#include <../acedb/gex.h>
-
-/* 
-
-Coordinates.
-
-We define two coordinate types.
-
-1) Coord: coordinates in the root object in the current direction.
-2) InvarCoord: coordinates in the root object in absolute direction.
-
-Seqregion can calculate a region on either the forward or reverse strand 
-of the root object. Most of the data it produces are Coords, these have the y
-property that they do not change as the region is expanded/contracted and that
-they increase the 5'->3' direction on the current strand. The latter property
-is important for drawing, but it means the _Coords_are_not_invariant_ over a 
-reverse-complement. All of the data-structures in seqRegion containing Coords 
-get re-calculated on rev-comp, so this is not a problem. 
-
-For calling code to store coordinates over a  rev-comp it is 
-necessary to use InvarCoords. Routines are supplied to convert between
-Coords and Invarcoords. Converting a Coord to an Invarcoord, 
-reverse-complementing and then converting back from InvarCoord to Coord
-will result in a new coordinate which points to the same base as the original.
-There is one gotcha to be aware of: consider an object with start and end
-coordinates, start < end as usual, and we store its identity as the 
-InvarCoord of the start. After a rev-comp we get the coord back, but it is now
-the _larger_ of the objects coordinates - ie the end coodinate.  
-
-*/
-
-typedef int Coord;
-typedef float ScreenCoord;
-typedef int InvarCoord;
-typedef int   VisibleCoord;
-
-typedef int methodID;
-
-typedef enum { NO_STRAND = 0, DOWN_STRAND, UP_STRAND } srStrand;
-typedef enum { NO_PHASE = 0, PHASE_0, PHASE_1, PHASE_2 } srPhase;
-typedef enum { 
-  SR_DEFAULT = 0, SR_HOMOL, SR_FEATURE,
-  SR_SEQUENCE, SR_TRANSCRIPT
-} srType;
-
-extern char dnaDecodeChar[] ;	/* this is the mapping used to decode a single base */
-
-/* structures *********************************************/
-/* zMapRegionStruct is the structure zmap expects to hold
- * all the data required for the display, so whatever is
- * providing the data must populate this structure. */
-
-struct zMapRegionStruct {
-  Coord area1, area2;
-  Array dna;
-  Array segs;
-  Array methods, oldMethods;
-  int length;
-  BOOL rootIsReverse;
-};
-
-typedef struct zMapRegionStruct ZMapRegion;
-
-/* zmap-flavour seg structure that holds the data to be displayed */
-
-struct segStruct {
-  char *id; /* stringBucket */
-  methodID method;
-  /* NOTE: srType BOTH discriminates the union below, _and_ controls
-     the sort of column made.  Two segs with the same method but
-     different types will end up in different columns. */
-  srType type;
-  srStrand strand;
-  srPhase phase;
-  float score;
-  Coord x1, x2;
-  union {
-    struct {
-      int y1, y2;
-      srStrand strand;
-      float score;
-      Array align;
-    } homol;
-    struct {
-      Coord cdsStart, cdsEnd;
-      BOOL endNotFound;
-      Array exons;
-    } transcript;
-    struct {
-      char *id; /* backpointer */
-    } exon;
-  } u;
-};
-
-typedef struct segStruct SEG;
-
-/* Coord structure */
-
-typedef struct {
-  Coord x1, x2;
-} srExon;
-
-typedef struct methodStruct
-{
-  methodID id;
-  char *name, *remark;
-  unsigned int flags;
-  int colour, CDS_colour, upStrandColour;
-  float minScore, maxScore;
-  float minMag, maxMag;
-  float width ;
-  char symbol ;
-  float priority;
-  float histBase;
-  BOOL showText, no_display;
-} srMeth;
-
-
-/* callback routines **************************************/
-/* This routine returns the initial set of zmap-flavour segs
- * when zmap is first called. */
-
-typedef void (*Activate_cb)(void *seqRegion,
-			    char *seqspec, 
-			    ZMapRegion *zMapRegion, 
-			    Coord *r1, 
-			    Coord *r2, 
-			    STORE_HANDLE *handle);
-
-/* This routine is called by the reverse-complement and
- * recalculate routines. */
-
-typedef void (*Calc_cb)    (void *seqRegion, 
-			    Coord x1, Coord x2,
-			    BOOL isReverse);
-     
-#endif  
-
-/************************ end of file *********************/