src/inc/gff3.h 1.2

Index: src/inc/gff3.h
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/inc/gff3.h,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 4 -r1.1 -r1.2
--- src/inc/gff3.h	22 Apr 2009 16:56:48 -0000	1.1
+++ src/inc/gff3.h	12 Aug 2009 07:48:05 -0000	1.2
@@ -90,10 +90,9 @@
     struct slName *parentIds; /* Indicates the parent of the feature.  A parent
                                * ID can be used to group exons into transcripts,
                                * transcripts into genes, an so forth.  A feature
                                * may have multiple parents.  Parent can *only* be
-                               * used to indicate a partof relationship. Value is
-                               * a null terminated array. */
+                               * used to indicate a partof relationship. */
     struct gff3AnnRef *parents; /* Parent objects for parentIds */
                                       
 
     char *targetId; /* Indicates the target of a nucleotide-to-nucleotide or
@@ -189,8 +188,31 @@
     int maxErr;             /* maximum number of errors before aborting */
     int errCnt;             /* error count */
 };
 
+
+/* standard attribute names */
+extern char *gff3AttrID;
+extern char *gff3AttrName;
+extern char *gff3AttrAlias;
+extern char *gff3AttrParent;
+extern char *gff3AttrTarget;
+extern char *gff3AttrGap;
+extern char *gff3AttrDerivesFrom;
+extern char *gff3AttrNote;
+extern char *gff3AttrDbxref;
+extern char *gff3AttrOntologyTerm;
+
+/* commonly used features names */
+extern char *gff3FeatGene;
+extern char *gff3FeatMRna;
+extern char *gff3FeatExon;
+extern char *gff3FeatCDS;
+extern char *gff3FeatThreePrimeUTR;
+extern char *gff3FeatFivePrimeUTR;
+extern char *gff3FeatStartCodon;
+extern char *gff3FeatStopCodon;
+
 struct gff3File *gff3FileOpen(char *fileName, int maxErr, FILE *errFh);
 /* Parse a GFF3 file into a gff3File object.  If maxErr not zero, then
  * continue to parse until this number of error have been reached.  A maxErr
  * less than zero does not stop reports all errors. Write errors to errFh,
@@ -207,5 +229,33 @@
 
 void gff3FileWrite(struct gff3File *g3f, char *fileName);
 /* write contents of an GFF3File object to a file */
 
+INLINE struct gff3AnnRef *gff3AnnRefNew(struct gff3Ann *g3a)
+/* Allocate a gff3AnnRef object from the heap.  Not used by the parsing code, as 
+ * all data is contained in localMem objects */
+{
+struct gff3AnnRef *ref;
+AllocVar(ref);
+ref->ann = g3a;
+return ref;
+}
+
+int gff3AnnRefLocCmp(const void *va, const void *vb);
+/* sort compare function for location of two gff3AnnRef objects */
+
+INLINE int gff3PhaseToFrame(int phase)
+/* convert a phase to a frame */
+{
+switch (phase)
+    {
+    case 0:
+        return 0;
+    case 1:
+        return 2;
+    case 2:
+        return 1;
+    }
+return -1;
+}
+
 #endif