initial version

src/include/ZMap/zmapFeature.h

+/*  File: zmapFeature.h
+ *  Author: Ed Griffiths (edgrif@sanger.ac.uk)
+ *  Copyright (c) Sanger Institute, 2004
+ *-------------------------------------------------------------------
+ * 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
+ * originated by
+ * 	Ed Griffiths (Sanger Institute, UK) edgrif@sanger.ac.uk,
+ *      Rob Clack (Sanger Institute, UK) rnc@sanger.ac.uk
+ *
+ * Description: Data structures describing a genetic feature.
+ *              
+ * HISTORY:
+ * Last edited: Jun 15 15:21 2004 (edgrif)
+ * Created: Fri Jun 11 08:37:19 2004 (edgrif)
+ * CVS info:   $Id: zmapFeature.h,v 1.1 2004-06-18 10:57:17 edgrif Exp $
+ *-------------------------------------------------------------------
+ */
+#ifndef ZMAP_FEATURE_H
+#define ZMAP_FEATURE_H
+
+#include <glib.h>
+
+/* A unique ID for each feature created, can be used to unabiguously query for that feature
+ * in a database. The feature id ZMAPFEATUREID_NULL is guaranteed not to equate to any feature
+ * and also means you can test using !(feature_id). */
+typedef unsigned int ZMapFeatureID ;
+enum {ZMAPFEATUREID_NULL = 0} ;
+
+
+typedef int Coord ;
+
+/* Unsure about this....probably should be some sort of key...... */
+typedef int methodID ;
+
+
+/* What about "sequence", atg, and allele as basic feature types ?           */
+typedef enum {ZMAPFEATURE_INVALID = -1,
+	      ZMAPFEATURE_BASIC = 0, ZMAPFEATURE_HOMOL,
+	      ZMAPFEATURE_EXON, ZMAPFEATURE_INTRON, 
+	      ZMAPFEATURE_TRANSCRIPT, ZMAPFEATURE_VARIATION,
+	      ZMAPFEATURE_BOUNDARY, ZMAPFEATURE_SEQUENCE} ZMapFeatureType ;
+
+typedef enum {ZMAPSTRAND_NONE = 0,
+	      ZMAPSTRAND_DOWN, ZMAPSTRAND_UP} ZMapStrand ;
+
+typedef enum {ZMAPPHASE_NONE = 0,
+	      ZMAPPHASE_0, ZMAPPHASE_1, ZMAPPHASE_2} ZMapPhase ;
+
+/* as in BLAST*, i.e. target is DNA, Protein, DNA translated */
+typedef enum {ZMAPHOMOL_N_HOMOL, ZMAPHOMOL_X_HOMOL, ZMAPHOMOL_TX_HOMOL} ZMapHomolType ;
+
+typedef enum {ZMAPBOUNDARY_CLONE_END, ZMAPBOUNDARY_5_SPLICE, ZMAPBOUNDARY_3_SPLICE } ZMapBoundaryType ;
+
+
+
+/* We have had this but would like to have a simple "span" sort....as below... */
+typedef struct
+{
+  Coord x1, x2 ;
+} ZMapExonStruct, *ZMapExon ;
+
+
+
+/* Could represent anything that has a span. */
+typedef struct
+{
+  Coord x1, x2 ;
+} ZMapSpanStruct, *ZMapSpan ;
+
+
+/* the following is used to store alignment gap information */
+typedef struct
+{
+  int q1, q2 ;						    /* coords in query sequence */
+  int t1, t2 ;						    /* coords in target sequence */
+} ZMapAlignBlock ;
+
+
+
+typedef struct
+{
+  ZMapHomolType type ;					    /* as in Blast* */
+  int y1, y2 ;						    /* target start/end */
+  ZMapStrand target_strand ;
+  ZMapPhase target_phase ;				    /* for tx_homol */
+  float score ;
+  GArray *align ;					    /* of AlignBlock, if null, align is ungapped. */
+} ZMapHomolStruct, *ZMapHomol ;
+
+
+typedef struct
+{
+  Coord cdsStart, cdsEnd ;
+  gboolean start_not_found ;
+  ZMapPhase cds_phase ;					    /* none if not a coding transcript ? */
+  gboolean endNotFound ;
+  GArray *exons ;
+  GArray *introns ;					    /* experiment...should we have
+							       explicit introns ? */
+} ZMapTranscriptStruct, *ZMapTranscript ;
+
+
+
+/* I don't know what this struct is for, I would guess that its to allow a floating exon to
+ * be linked to some sort of feature ? */
+typedef struct
+{
+  ZMapFeatureID *id ;					    /* backpointer */
+} ZMapSingleExonStruct, *ZMapSingleExon ;
+
+
+
+
+
+
+
+/* zmap-flavour seg structure that holds the data to be displayed */
+
+typedef struct ZMapFeatureStruct_ 
+{
+  ZMapFeatureID id ;					    /* unique DB identifier. */
+  char *name ;						    /* e.g. "bA404F10.4.mRNA" */
+  ZMapFeatureType type ;				    /* e.g. intron, homol etc. */
+
+  Coord x1, x2 ;					    /* start, end of feature in absolute coords. */
+
+  methodID method ;					    /* i.e. the "column" type */
+  char *method_name ;					    /* temp...replace with quark ? */
+
+  /* um, I'm not sure this is correct, surely a column is a column and the only thing that matters
+   * is the 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. */
+
+  ZMapStrand strand ;
+  ZMapPhase phase ;
+  float score ;
+  char *text ;						    /* needed ????? */
+
+  union
+  {
+    ZMapHomolStruct homol ;
+    ZMapTranscriptStruct transcript ;
+    ZMapSingleExonStruct exon ;				    /* What is this needed for ? */
+  } feature ;
+
+} ZMapFeatureStruct, *ZMapFeature ;
+
+
+
+
+/* Holds a set of features. */
+typedef struct ZMapFeatureSetStruct_
+{
+  char *source ;					    /* e.g. "Genewise predictions" */
+
+  GArray *features ;					    /* An array of ZMapFeatureStruct. */
+
+} ZMapFeatureSetStruct, *ZMapFeatureSet ;
+
+
+
+
+
+
+
+#ifdef ED_G_NEVER_INCLUDE_THIS_CODE
+
+/* CURRENTLY NOT NEEDED I THINK...... */
+
+
+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 /* ED_G_NEVER_INCLUDE_THIS_CODE */
+     
+
+#endif /* ZMAP_FEATURE_H */