text: /* fishClones.c was originally generated by the autoSql program, which also 
   * generated fishClones.h and fishClones.sql.  This module links the database and
   * the RAM representation of objects. */
  
  #include "common.h"
  #include "linefile.h"
  #include "jksql.h"
  #include "fishClones.h"
  
  
  struct fishClones *fishClonesLoad(char **row)
  /* Load a fishClones from row fetched with select * from fishClones
   * from database.  Dispose of this with fishClonesFree(). */
  {
  struct fishClones *ret;
  int sizeOne;
  
  AllocVar(ret);
  ret->placeCount = sqlUnsigned(row[5]);
  ret->accCount = sqlUnsigned(row[10]);
  ret->stsCount = sqlUnsigned(row[12]);
  ret->beCount = sqlUnsigned(row[14]);
  ret->chrom = cloneString(row[0]);
  ret->chromStart = sqlUnsigned(row[1]);
  ret->chromEnd = sqlUnsigned(row[2]);
  ret->name = cloneString(row[3]);
  ret->score = sqlUnsigned(row[4]);
  sqlStringDynamicArray(row[6], &ret->bandStarts, &sizeOne);
  assert(sizeOne == ret->placeCount);
  sqlStringDynamicArray(row[7], &ret->bandEnds, &sizeOne);
  assert(sizeOne == ret->placeCount);
  sqlStringDynamicArray(row[8], &ret->labs, &sizeOne);
  assert(sizeOne == ret->placeCount);
  ret->placeType = cloneString(row[9]);
  sqlStringDynamicArray(row[11], &ret->accNames, &sizeOne);
  assert(sizeOne == ret->accCount);
  sqlStringDynamicArray(row[13], &ret->stsNames, &sizeOne);
  assert(sizeOne == ret->stsCount);
  sqlStringDynamicArray(row[15], &ret->beNames, &sizeOne);
  assert(sizeOne == ret->beCount);
  return ret;
  }
  
  struct fishClones *fishClonesLoadAll(char *fileName) 
  /* Load all fishClones from a tab-separated file.
   * Dispose of this with fishClonesFreeList(). */
  {
  struct fishClones *list = NULL, *el;
  struct lineFile *lf = lineFileOpen(fileName, TRUE);
  char *row[16];
  
  while (lineFileRow(lf, row))
      {
      el = fishClonesLoad(row);
      slAddHead(&list, el);
      }
  lineFileClose(&lf);
  slReverse(&list);
  return list;
  }
  
  struct fishClones *fishClonesCommaIn(char **pS, struct fishClones *ret)
  /* Create a fishClones out of a comma separated string. 
   * This will fill in ret if non-null, otherwise will
   * return a new fishClones */
  {
  char *s = *pS;
  int i;
  
  if (ret == NULL)
      AllocVar(ret);
  ret->chrom = sqlStringComma(&s);
  ret->chromStart = sqlUnsignedComma(&s);
  ret->chromEnd = sqlUnsignedComma(&s);
  ret->name = sqlStringComma(&s);
  ret->score = sqlUnsignedComma(&s);
  ret->placeCount = sqlUnsignedComma(&s);
  s = sqlEatChar(s, '{');
  AllocArray(ret->bandStarts, ret->placeCount);
  for (i=0; i<ret->placeCount; ++i)
      {
      ret->bandStarts[i] = sqlStringComma(&s);
      }
  s = sqlEatChar(s, '}');
  s = sqlEatChar(s, ',');
  s = sqlEatChar(s, '{');
  AllocArray(ret->bandEnds, ret->placeCount);
  for (i=0; i<ret->placeCount; ++i)
      {
      ret->bandEnds[i] = sqlStringComma(&s);
      }
  s = sqlEatChar(s, '}');
  s = sqlEatChar(s, ',');
  s = sqlEatChar(s, '{');
  AllocArray(ret->labs, ret->placeCount);
  for (i=0; i<ret->placeCount; ++i)
      {
      ret->labs[i] = sqlStringComma(&s);
      }
  s = sqlEatChar(s, '}');
  s = sqlEatChar(s, ',');
  ret->placeType = sqlStringComma(&s);
  ret->accCount = sqlUnsignedComma(&s);
  s = sqlEatChar(s, '{');
  AllocArray(ret->accNames, ret->accCount);
  for (i=0; i<ret->accCount; ++i)
      {
      ret->accNames[i] = sqlStringComma(&s);
      }
  s = sqlEatChar(s, '}');
  s = sqlEatChar(s, ',');
  ret->stsCount = sqlUnsignedComma(&s);
  s = sqlEatChar(s, '{');
  AllocArray(ret->stsNames, ret->stsCount);
  for (i=0; i<ret->stsCount; ++i)
      {
      ret->stsNames[i] = sqlStringComma(&s);
      }
  s = sqlEatChar(s, '}');
  s = sqlEatChar(s, ',');
  ret->beCount = sqlUnsignedComma(&s);
  s = sqlEatChar(s, '{');
  AllocArray(ret->beNames, ret->beCount);
  for (i=0; i<ret->beCount; ++i)
      {
      ret->beNames[i] = sqlStringComma(&s);
      }
  s = sqlEatChar(s, '}');
  s = sqlEatChar(s, ',');
  *pS = s;
  return ret;
  }
  
  void fishClonesFree(struct fishClones **pEl)
  /* Free a single dynamically allocated fishClones such as created
   * with fishClonesLoad(). */
  {
  struct fishClones *el;
  
  if ((el = *pEl) == NULL) return;
  freeMem(el->chrom);
  freeMem(el->name);
  /* All strings in bandStarts are allocated at once, so only need to free first. */
  if (el->bandStarts != NULL)
      freeMem(el->bandStarts[0]);
  freeMem(el->bandStarts);
  /* All strings in bandEnds are allocated at once, so only need to free first. */
  if (el->bandEnds != NULL)
      freeMem(el->bandEnds[0]);
  freeMem(el->bandEnds);
  /* All strings in labs are allocated at once, so only need to free first. */
  if (el->labs != NULL)
      freeMem(el->labs[0]);
  freeMem(el->labs);
  freeMem(el->placeType);
  /* All strings in accNames are allocated at once, so only need to free first. */
  if (el->accNames != NULL)
      freeMem(el->accNames[0]);
  freeMem(el->accNames);
  /* All strings in stsNames are allocated at once, so only need to free first. */
  if (el->stsNames != NULL)
      freeMem(el->stsNames[0]);
  freeMem(el->stsNames);
  /* All strings in beNames are allocated at once, so only need to free first. */
  if (el->beNames != NULL)
      freeMem(el->beNames[0]);
  freeMem(el->beNames);
  freez(pEl);
  }
  
  void fishClonesFreeList(struct fishClones **pList)
  /* Free a list of dynamically allocated fishClones's */
  {
  struct fishClones *el, *next;
  
  for (el = *pList; el != NULL; el = next)
      {
      next = el->next;
      fishClonesFree(&el);
      }
  *pList = NULL;
  }
  
  void fishClonesOutput(struct fishClones *el, FILE *f, char sep, char lastSep) 
  /* Print out fishClones.  Separate fields with sep. Follow last field with lastSep. */
  {
  int i;
  if (sep == ',') fputc('"',f);
  fprintf(f, "%s", el->chrom);
  if (sep == ',') fputc('"',f);
  fputc(sep,f);
  fprintf(f, "%u", el->chromStart);
  fputc(sep,f);
  fprintf(f, "%u", el->chromEnd);
  fputc(sep,f);
  if (sep == ',') fputc('"',f);
  fprintf(f, "%s", el->name);
  if (sep == ',') fputc('"',f);
  fputc(sep,f);
  fprintf(f, "%u", el->score);
  fputc(sep,f);
  fprintf(f, "%u", el->placeCount);
  fputc(sep,f);
  if (sep == ',') fputc('{',f);
  for (i=0; i<el->placeCount; ++i)
      {
      if (sep == ',') fputc('"',f);
      fprintf(f, "%s", el->bandStarts[i]);
      if (sep == ',') fputc('"',f);
      fputc(',', f);
      }
  if (sep == ',') fputc('}',f);
  fputc(sep,f);
  if (sep == ',') fputc('{',f);
  for (i=0; i<el->placeCount; ++i)
      {
      if (sep == ',') fputc('"',f);
      fprintf(f, "%s", el->bandEnds[i]);
      if (sep == ',') fputc('"',f);
      fputc(',', f);
      }
  if (sep == ',') fputc('}',f);
  fputc(sep,f);
  if (sep == ',') fputc('{',f);
  for (i=0; i<el->placeCount; ++i)
      {
      if (sep == ',') fputc('"',f);
      fprintf(f, "%s", el->labs[i]);
      if (sep == ',') fputc('"',f);
      fputc(',', f);
      }
  if (sep == ',') fputc('}',f);
  fputc(sep,f);
  if (sep == ',') fputc('"',f);
  fprintf(f, "%s", el->placeType);
  if (sep == ',') fputc('"',f);
  fputc(sep,f);
  fprintf(f, "%u", el->accCount);
  fputc(sep,f);
  if (sep == ',') fputc('{',f);
  for (i=0; i<el->accCount; ++i)
      {
      if (sep == ',') fputc('"',f);
      fprintf(f, "%s", el->accNames[i]);
      if (sep == ',') fputc('"',f);
      fputc(',', f);
      }
  if (sep == ',') fputc('}',f);
  fputc(sep,f);
  fprintf(f, "%u", el->stsCount);
  fputc(sep,f);
  if (sep == ',') fputc('{',f);
  for (i=0; i<el->stsCount; ++i)
      {
      if (sep == ',') fputc('"',f);
      fprintf(f, "%s", el->stsNames[i]);
      if (sep == ',') fputc('"',f);
      fputc(',', f);
      }
  if (sep == ',') fputc('}',f);
  fputc(sep,f);
  fprintf(f, "%u", el->beCount);
  fputc(sep,f);
  if (sep == ',') fputc('{',f);
  for (i=0; i<el->beCount; ++i)
      {
      if (sep == ',') fputc('"',f);
      fprintf(f, "%s", el->beNames[i]);
      if (sep == ',') fputc('"',f);
      fputc(',', f);
      }
  if (sep == ',') fputc('}',f);
  fputc(lastSep,f);
  }
  
  