text: /* ccdsGeneMap.h was originally generated by the autoSql program, which also 
   * generated ccdsGeneMap.c and ccdsGeneMap.sql.  This header links the database and
   * the RAM representation of objects. */
  
  /* Copyright (C) 2007 The Regents of the University of California 
   * See README in this or parent directory for licensing information. */
  
  #ifndef CCDSGENEMAP_H
  #define CCDSGENEMAP_H
  
  #define CCDSGENEMAP_NUM_COLS 6
  
  struct ccdsGeneMap
  /* mapping between CCDS ids and other gene tables by similarity */
      {
      struct ccdsGeneMap *next;  /* Next in singly linked list. */
      char *ccdsId;	/* CCDS id with version  */
      char *geneId;	/* Id of other gene */
      char *chrom;	/* chromosome of other gene */
      unsigned chromStart;	/* chromosome start of other gene */
      unsigned chromEnd;	/* chromosome end of other gene */
      float cdsSimilarity;	/* CDS similarity by genomic overlap */
      };
  
  void ccdsGeneMapStaticLoad(char **row, struct ccdsGeneMap *ret);
  /* Load a row from ccdsGeneMap table into ret.  The contents of ret will
   * be replaced at the next call to this function. */
  
  struct ccdsGeneMap *ccdsGeneMapLoad(char **row);
  /* Load a ccdsGeneMap from row fetched with select * from ccdsGeneMap
   * from database.  Dispose of this with ccdsGeneMapFree(). */
  
  struct ccdsGeneMap *ccdsGeneMapLoadAll(char *fileName);
  /* Load all ccdsGeneMap from whitespace-separated file.
   * Dispose of this with ccdsGeneMapFreeList(). */
  
  struct ccdsGeneMap *ccdsGeneMapLoadAllByChar(char *fileName, char chopper);
  /* Load all ccdsGeneMap from chopper separated file.
   * Dispose of this with ccdsGeneMapFreeList(). */
  
  #define ccdsGeneMapLoadAllByTab(a) ccdsGeneMapLoadAllByChar(a, '\t');
  /* Load all ccdsGeneMap from tab separated file.
   * Dispose of this with ccdsGeneMapFreeList(). */
  
  struct ccdsGeneMap *ccdsGeneMapCommaIn(char **pS, struct ccdsGeneMap *ret);
  /* Create a ccdsGeneMap out of a comma separated string. 
   * This will fill in ret if non-null, otherwise will
   * return a new ccdsGeneMap */
  
  void ccdsGeneMapFree(struct ccdsGeneMap **pEl);
  /* Free a single dynamically allocated ccdsGeneMap such as created
   * with ccdsGeneMapLoad(). */
  
  void ccdsGeneMapFreeList(struct ccdsGeneMap **pList);
  /* Free a list of dynamically allocated ccdsGeneMap's */
  
  void ccdsGeneMapOutput(struct ccdsGeneMap *el, FILE *f, char sep, char lastSep);
  /* Print out ccdsGeneMap.  Separate fields with sep. Follow last field with lastSep. */
  
  #define ccdsGeneMapTabOut(el,f) ccdsGeneMapOutput(el,f,'\t','\n');
  /* Print out ccdsGeneMap as a line in a tab-separated file. */
  
  #define ccdsGeneMapCommaOut(el,f) ccdsGeneMapOutput(el,f,',',',');
  /* Print out ccdsGeneMap as a comma separated list including final comma. */
  
  /* -------------------------------- End autoSql Generated Code -------------------------------- */
  
  char *ccdsGeneMapGetCreateSql(char *table);
  /* Get SQL command to create ccdsGeneMap table. Result should be freed. */
  
  struct ccdsGeneMap *ccdsGeneMapSelectByCcds(struct sqlConnection *conn, char *mapTable,
                                              char *ccdsId, char *chrom, float minSimilarity);
  /* select ccdsGeneMap records by ccds and minimum CDS similarity from the
   * specified table. */
  
  struct ccdsGeneMap *ccdsGeneMapSelectByGene(struct sqlConnection *conn, char *mapTable,
                                              char *geneId, float minSimilarity);
  /* select ccdsGeneMap records by gene id and minimum CDS similarity from the
   * specified table. */
  
  struct ccdsGeneMap *ccdsGeneMapSelectByGeneOver(struct sqlConnection *conn, char *mapTable,
                                                  char *geneId, char *chrom, unsigned chromStart,
                                                  unsigned chromEnd, float minSimilarity);
  /* select ccdsGeneMap records by gene id, location overlap, and minimum CDS
   * similarity from the specified table. */
  
  int ccdsGeneMapSimilarityCmp(const void *va, const void *vb);
  /* compare based on descending similarity */
  
  int ccdsGeneMapCcdsIdCmp(const void *va, const void *vb);
  /* compare based on gene id */
  
  int ccdsGeneMapGeneIdCmp(const void *va, const void *vb);
  /* compare based on gene id */
  
  #endif /* CCDSGENEMAP_H */
  
  