text: /* liftOverChain.c was originally generated by the autoSql program, which also 
   * generated liftOverChain.h and liftOverChain.sql.  This module links the database and
   * the RAM representation of objects. */
  
  #include "common.h"
  #include "linefile.h"
  #include "dystring.h"
  #include "jksql.h"
  #include "liftOverChain.h"
  
  static char const rcsid[] = "$Id: liftOverChain.c,v 1.5 2006/07/11 05:51:39 kate Exp $";
  
  void liftOverChainStaticLoad(char **row, struct liftOverChain *ret)
  /* Load a row from liftOverChain table into ret.  The contents of ret will
   * be replaced at the next call to this function. */
  {
  
  ret->fromDb = row[0];
  ret->toDb = row[1];
  ret->path = row[2];
  ret->minMatch = atof(row[3]);
  ret->minSizeT = sqlUnsigned(row[4]);
  ret->minSizeQ = sqlUnsigned(row[5]);
  strcpy(ret->multiple, row[6]);
  ret->minBlocks = atof(row[7]);
  strcpy(ret->fudgeThick, row[8]);
  }
  
  struct liftOverChain *liftOverChainLoad(char **row)
  /* Load a liftOverChain from row fetched with select * from liftOverChain
   * from database.  Dispose of this with liftOverChainFree(). */
  {
  struct liftOverChain *ret;
  
  AllocVar(ret);
  ret->fromDb = cloneString(row[0]);
  ret->toDb = cloneString(row[1]);
  ret->path = cloneString(row[2]);
  ret->minMatch = atof(row[3]);
  ret->minSizeT = sqlUnsigned(row[4]);
  ret->minSizeQ = sqlUnsigned(row[5]);
  strcpy(ret->multiple, row[6]);
  ret->minBlocks = atof(row[7]);
  strcpy(ret->fudgeThick, row[8]);
  return ret;
  }
  
  struct liftOverChain *liftOverChainLoadAll(char *fileName) 
  /* Load all liftOverChain from a whitespace-separated file.
   * Dispose of this with liftOverChainFreeList(). */
  {
  struct liftOverChain *list = NULL, *el;
  struct lineFile *lf = lineFileOpen(fileName, TRUE);
  char *row[9];
  
  while (lineFileRow(lf, row))
      {
      el = liftOverChainLoad(row);
      slAddHead(&list, el);
      }
  lineFileClose(&lf);
  slReverse(&list);
  return list;
  }
  
  struct liftOverChain *liftOverChainLoadAllByChar(char *fileName, char chopper) 
  /* Load all liftOverChain from a chopper separated file.
   * Dispose of this with liftOverChainFreeList(). */
  {
  struct liftOverChain *list = NULL, *el;
  struct lineFile *lf = lineFileOpen(fileName, TRUE);
  char *row[9];
  
  while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
      {
      el = liftOverChainLoad(row);
      slAddHead(&list, el);
      }
  lineFileClose(&lf);
  slReverse(&list);
  return list;
  }
  
  struct liftOverChain *liftOverChainLoadByQuery(struct sqlConnection *conn, char *query)
  /* Load all liftOverChain from table that satisfy the query given.  
   * Where query is of the form 'select * from example where something=something'
   * or 'select example.* from example, anotherTable where example.something = 
   * anotherTable.something'.
   * Dispose of this with liftOverChainFreeList(). */
  {
  struct liftOverChain *list = NULL, *el;
  struct sqlResult *sr;
  char **row;
  
  sr = sqlGetResult(conn, query);
  while ((row = sqlNextRow(sr)) != NULL)
      {
      el = liftOverChainLoad(row);
      slAddHead(&list, el);
      }
  slReverse(&list);
  sqlFreeResult(&sr);
  return list;
  }
  
  void liftOverChainSaveToDb(struct sqlConnection *conn, struct liftOverChain *el, char *tableName, int updateSize)
  /* Save liftOverChain as a row to the table specified by tableName. 
   * As blob fields may be arbitrary size updateSize specifies the approx size
   * of a string that would contain the entire query. Arrays of native types are
   * converted to comma separated strings and loaded as such, User defined types are
   * inserted as NULL. Note that strings must be escaped to allow insertion into the database.
   * For example "autosql's features include" --> "autosql\'s features include" 
   * If worried about this use liftOverChainSaveToDbEscaped() */
  {
  struct dyString *update = newDyString(updateSize);
  dyStringPrintf(update, "insert into %s values ( '%s','%s',%s,%g,%u,%u,'%s',%g,'%s')", 
  	tableName,  el->fromDb,  el->toDb,  el->path,  el->minMatch,  el->minSizeT,  el->minSizeQ,  el->multiple,  el->minBlocks,  el->fudgeThick);
  sqlUpdate(conn, update->string);
  freeDyString(&update);
  }
  
  void liftOverChainSaveToDbEscaped(struct sqlConnection *conn, struct liftOverChain *el, char *tableName, int updateSize)
  /* Save liftOverChain as a row to the table specified by tableName. 
   * As blob fields may be arbitrary size updateSize specifies the approx size.
   * of a string that would contain the entire query. Automatically 
   * escapes all simple strings (not arrays of string) but may be slower than liftOverChainSaveToDb().
   * For example automatically copies and converts: 
   * "autosql's features include" --> "autosql\'s features include" 
   * before inserting into database. */ 
  {
  struct dyString *update = newDyString(updateSize);
  char  *fromDb, *toDb, *path, *multiple, *fudgeThick;
  fromDb = sqlEscapeString(el->fromDb);
  toDb = sqlEscapeString(el->toDb);
  path = sqlEscapeString(el->path);
  multiple = sqlEscapeString(el->multiple);
  fudgeThick = sqlEscapeString(el->fudgeThick);
  
  dyStringPrintf(update, "insert into %s values ( '%s','%s','%s',%g,%u,%u,'%s',%g,'%s')", 
  	tableName,  fromDb,  toDb,  path, el->minMatch , el->minSizeT , el->minSizeQ ,  multiple, el->minBlocks ,  fudgeThick);
  sqlUpdate(conn, update->string);
  freeDyString(&update);
  freez(&fromDb);
  freez(&toDb);
  freez(&path);
  freez(&multiple);
  freez(&fudgeThick);
  }
  
  struct liftOverChain *liftOverChainCommaIn(char **pS, struct liftOverChain *ret)
  /* Create a liftOverChain out of a comma separated string. 
   * This will fill in ret if non-null, otherwise will
   * return a new liftOverChain */
  {
  char *s = *pS;
  
  if (ret == NULL)
      AllocVar(ret);
  ret->fromDb = sqlStringComma(&s);
  ret->toDb = sqlStringComma(&s);
  ret->path = sqlStringComma(&s);
  ret->minMatch = sqlFloatComma(&s);
  ret->minSizeT = sqlUnsignedComma(&s);
  ret->minSizeQ = sqlUnsignedComma(&s);
  sqlFixedStringComma(&s, ret->multiple, sizeof(ret->multiple));
  ret->minBlocks = sqlFloatComma(&s);
  sqlFixedStringComma(&s, ret->fudgeThick, sizeof(ret->fudgeThick));
  *pS = s;
  return ret;
  }
  
  void liftOverChainFree(struct liftOverChain **pEl)
  /* Free a single dynamically allocated liftOverChain such as created
   * with liftOverChainLoad(). */
  {
  struct liftOverChain *el;
  
  if ((el = *pEl) == NULL) return;
  freeMem(el->fromDb);
  freeMem(el->toDb);
  freeMem(el->path);
  freez(pEl);
  }
  
  void liftOverChainFreeList(struct liftOverChain **pList)
  /* Free a list of dynamically allocated liftOverChain's */
  {
  struct liftOverChain *el, *next;
  
  for (el = *pList; el != NULL; el = next)
      {
      next = el->next;
      liftOverChainFree(&el);
      }
  *pList = NULL;
  }
  
  void liftOverChainOutput(struct liftOverChain *el, FILE *f, char sep, char lastSep) 
  /* Print out liftOverChain.  Separate fields with sep. Follow last field with lastSep. */
  {
  if (sep == ',') fputc('"',f);
  fprintf(f, "%s", el->fromDb);
  if (sep == ',') fputc('"',f);
  fputc(sep,f);
  if (sep == ',') fputc('"',f);
  fprintf(f, "%s", el->toDb);
  if (sep == ',') fputc('"',f);
  fputc(sep,f);
  if (sep == ',') fputc('"',f);
  fprintf(f, "%s", el->path);
  if (sep == ',') fputc('"',f);
  fputc(sep,f);
  fprintf(f, "%g", el->minMatch);
  fputc(sep,f);
  fprintf(f, "%u", el->minSizeT);
  fputc(sep,f);
  fprintf(f, "%u", el->minSizeQ);
  fputc(sep,f);
  if (sep == ',') fputc('"',f);
  fprintf(f, "%s", el->multiple);
  if (sep == ',') fputc('"',f);
  fputc(sep,f);
  fprintf(f, "%g", el->minBlocks);
  fputc(sep,f);
  if (sep == ',') fputc('"',f);
  fprintf(f, "%s", el->fudgeThick);
  if (sep == ',') fputc('"',f);
  fputc(lastSep,f);
  }
  
  /* -------------------------------- End autoSql Generated Code -------------------------------- */
  
  boolean liftOverChainExists(struct sqlConnection *conn, char *tableName,
                                  char *fromDb, char *toDb)
  /* Return TRUE if row where fromDb and toDb match */
  {
  char query[256];
  safef(query, sizeof(query), 
          "select count(*) from %s where fromDb = '%s' and toDb = '%s'",
  	        tableName, fromDb, toDb);
  return sqlQuickNum(conn, query) > 0;
  }
  
  void liftOverChainRemove(struct sqlConnection *conn, char *tableName,
                                  char *fromDb, char *toDb)
  /* Remove rows where fromDb and toDb match */
  {
  char query[256];
  safef(query, sizeof(query), 
          "delete from %s where fromDb = '%s' and toDb = '%s'",
  	        tableName, fromDb, toDb);
  sqlUpdate(conn, query);
  }
  