b95ff3835509b242bd9007ba55c4f60c1022da47
markd
  Thu Dec 30 14:58:16 2010 -0800
moved to programs to hg/utils, fixed build of distributed utilities
diff --git src/hg/overlapSelect/chromAnn.h src/hg/overlapSelect/chromAnn.h
deleted file mode 100644
index 0cba7a8..0000000
--- src/hg/overlapSelect/chromAnn.h
+++ /dev/null
@@ -1,115 +0,0 @@
-/* chromAnn - chomosome annotations, generic object to store annotations from
- * other formats */
-#ifndef CHROMANN_H
-#define CHROMANN_H
-struct rowReader;
-struct coordCols;
-
-enum chromAnnOpts
-/* bit set of options */ 
-{
-    chromAnnCds        = 0x01,  /* use only CDS in blocks */
-    chromAnnRange      = 0x02,  /* save entire range, not just blocks */
-    chromAnnSaveLines  = 0x04,  /* save records as lines os they can be
-                                 * outputted latter */
-    chromAnnUseQSide   = 0x08   /* use query side of alignment */
-};
-
-struct chromAnn
-/* chomosome annotations, generic object to store annotations from other
- * formats */
-{
-    struct chromAnn *next;
-    char* name;      /* optional name of the item */
-    char* chrom;     /* object coordinates */
-    char strand;
-    int start;       /* start of first block */
-    int end;         /* end of last block */
-    int totalSize;   /* size of all blocks */
-    void *rec;       /* record that can be used to recreate the data */
-    void (*recWrite)(struct chromAnn *ca, FILE *fh, char term); /* write record to file, with term character */
-    void (*recFree)(struct chromAnn *ca);  /* free function for rec */
-    struct chromAnnBlk *blocks;  /* ranges associated with this object */
-    boolean used;    /* flag to indicated that this chromAnn has been used */
-};
-
-struct chromAnnRef
-/* chromAnn reference list element */
-{
-    struct chromAnnRef *next;
-    struct chromAnn *ref;
-};
-
-struct chromAnnBlk
-/* specifies a range to select */
-{
-    struct chromAnnBlk *next;
-    struct chromAnn *ca;  /* link back to chromAnn */
-    int start;            /* block coordinates */
-    int end;
-};
-
-struct chromAnnReader
-/* interface object used to read chromAnn objects from various formats */
-{
-    struct chromAnn* (*caRead)(struct chromAnnReader *car);
-    /* read the next object, returns NULL on eof */
-
-    void (*carFree)(struct chromAnnReader **carPtr);
-    /* function to free this object */
-
-    unsigned opts;  /* options for reader */
-    void *data;     /* data associated with this reader */
-};
-
-void chromAnnFree(struct chromAnn **caPtr);
-/* free an object */
-
-int chromAnnTotalBlockSize(struct chromAnn* ca);
-/* count the total bases in the blocks of a chromAnn */
-
-struct chromAnnReader *chromAnnBedReaderNew(char *fileName, unsigned opts);
-/* construct a reader for a BED file */
-
-struct chromAnnReader *chromAnnGenePredReaderNew(char *fileName, unsigned opts);
-/* construct a reader for a genePred file */
-
-struct chromAnnReader *chromAnnPslReaderNew(char *fileName, unsigned opts);
-/* construct a reader for a PSL file */
-
-struct chromAnnReader *chromAnnChainReaderNew(char *fileName, unsigned opts);
-/* construct a reader for a chain file */
-
-struct chromAnnReader *chromAnnTabReaderNew(char *fileName, struct coordCols* cols, unsigned opts);
-/* construct a reader for an arbitrary tab file */
-
-INLINE struct chromAnnRef *chromAnnRefNew(struct chromAnn *chromAnn)
-/* construct a new chromAnnRef */
-{
-struct chromAnnRef *car;
-AllocVar(car);
-car->ref = chromAnn;
-return car;
-}
-
-INLINE boolean chromAnnOnList(struct chromAnnRef *refList, struct chromAnn *chromAnn)
-/* check in chromAnn is on list */
-{
-struct chromAnnRef *ref;
-for (ref = refList; ref != NULL; ref = ref->next)
-    if (ref->ref == chromAnn)
-        return TRUE;
-return FALSE;
-}
-
-INLINE void chromAnnRefAdd(struct chromAnnRef **refList, struct chromAnn *chromAnn)
-/* add a chromAnn to the list, if it isn't already there  */
-{
-if (!chromAnnOnList(*refList, chromAnn))
-    slSafeAddHead(refList, chromAnnRefNew(chromAnn));
-}
-
-int chromAnnRefLocCmp(const void *va, const void *vb);
-/* Compare location of two chromAnnRef objects. */
-
-#endif