text: /* snp125.c was originally generated by the autoSql program, which also 
   * generated snp125.h and snp125.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 "snp125.h"
  
  
  void snp125StaticLoad(char **row, struct snp125 *ret)
  /* Load a row from snp125 table into ret.  The contents of ret will
   * be replaced at the next call to this function. */
  {
  
  ret->chrom = row[0];
  ret->chromStart = sqlUnsigned(row[1]);
  ret->chromEnd = sqlUnsigned(row[2]);
  ret->name = row[3];
  ret->score = sqlUnsigned(row[4]);
  ret->strand = row[5];
  ret->refNCBI = row[6];
  ret->refUCSC = row[7];
  ret->observed = row[8];
  ret->molType = row[9];
  ret->class = row[10];
  ret->valid = row[11];
  ret->avHet = atof(row[12]);
  ret->avHetSE = atof(row[13]);
  ret->func = row[14];
  ret->locType = row[15];
  ret->weight = sqlUnsigned(row[16]);
  }
  
  struct snp125 *snp125Load(char **row)
  /* Load a snp125 from row fetched with select * from snp125
   * from database.  Dispose of this with snp125Free(). */
  {
  struct snp125 *ret;
  
  AllocVar(ret);
  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]);
  ret->strand = cloneString(row[5]);
  ret->refNCBI = cloneString(row[6]);
  ret->refUCSC = cloneString(row[7]);
  ret->observed = cloneString(row[8]);
  ret->molType = cloneString(row[9]);
  ret->class = cloneString(row[10]);
  ret->valid = cloneString(row[11]);
  ret->avHet = atof(row[12]);
  ret->avHetSE = atof(row[13]);
  ret->func = cloneString(row[14]);
  ret->locType = cloneString(row[15]);
  ret->weight = sqlUnsigned(row[16]);
  return ret;
  }
  
  struct snp125 *snp125LoadAll(char *fileName) 
  /* Load all snp125 from a whitespace-separated file.
   * Dispose of this with snp125FreeList(). */
  {
  struct snp125 *list = NULL, *el;
  struct lineFile *lf = lineFileOpen(fileName, TRUE);
  char *row[17];
  
  while (lineFileRow(lf, row))
      {
      el = snp125Load(row);
      slAddHead(&list, el);
      }
  lineFileClose(&lf);
  slReverse(&list);
  return list;
  }
  
  struct snp125 *snp125LoadAllByChar(char *fileName, char chopper) 
  /* Load all snp125 from a chopper separated file.
   * Dispose of this with snp125FreeList(). */
  {
  struct snp125 *list = NULL, *el;
  struct lineFile *lf = lineFileOpen(fileName, TRUE);
  char *row[17];
  
  while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
      {
      el = snp125Load(row);
      slAddHead(&list, el);
      }
  lineFileClose(&lf);
  slReverse(&list);
  return list;
  }
  
  struct snp125 *snp125CommaIn(char **pS, struct snp125 *ret)
  /* Create a snp125 out of a comma separated string. 
   * This will fill in ret if non-null, otherwise will
   * return a new snp125 */
  {
  char *s = *pS;
  
  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->strand = sqlStringComma(&s);
  ret->refNCBI = sqlStringComma(&s);
  ret->refUCSC = sqlStringComma(&s);
  ret->observed = sqlStringComma(&s);
  ret->molType = sqlStringComma(&s);
  ret->class = sqlStringComma(&s);
  ret->valid = sqlStringComma(&s);
  ret->avHet = sqlFloatComma(&s);
  ret->avHetSE = sqlFloatComma(&s);
  ret->func = sqlStringComma(&s);
  ret->locType = sqlStringComma(&s);
  ret->weight = sqlUnsignedComma(&s);
  *pS = s;
  return ret;
  }
  
  void snp125Free(struct snp125 **pEl)
  /* Free a single dynamically allocated snp125 such as created
   * with snp125Load(). */
  {
  struct snp125 *el;
  
  if ((el = *pEl) == NULL) return;
  freeMem(el->chrom);
  freeMem(el->name);
  freeMem(el->strand);
  freeMem(el->refNCBI);
  freeMem(el->refUCSC);
  freeMem(el->observed);
  freeMem(el->molType);
  freeMem(el->class);
  freeMem(el->valid);
  freeMem(el->func);
  freeMem(el->locType);
  freez(pEl);
  }
  
  void snp125FreeList(struct snp125 **pList)
  /* Free a list of dynamically allocated snp125's */
  {
  struct snp125 *el, *next;
  
  for (el = *pList; el != NULL; el = next)
      {
      next = el->next;
      snp125Free(&el);
      }
  *pList = NULL;
  }
  
  void snp125Output(struct snp125 *el, FILE *f, char sep, char lastSep) 
  /* Print out snp125.  Separate fields with sep. Follow last field with lastSep. */
  {
  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);
  if (sep == ',') fputc('"',f);
  fprintf(f, "%s", el->strand);
  if (sep == ',') fputc('"',f);
  fputc(sep,f);
  if (sep == ',') fputc('"',f);
  fprintf(f, "%s", el->refNCBI);
  if (sep == ',') fputc('"',f);
  fputc(sep,f);
  if (sep == ',') fputc('"',f);
  fprintf(f, "%s", el->refUCSC);
  if (sep == ',') fputc('"',f);
  fputc(sep,f);
  if (sep == ',') fputc('"',f);
  fprintf(f, "%s", el->observed);
  if (sep == ',') fputc('"',f);
  fputc(sep,f);
  if (sep == ',') fputc('"',f);
  fprintf(f, "%s", el->molType);
  if (sep == ',') fputc('"',f);
  fputc(sep,f);
  if (sep == ',') fputc('"',f);
  fprintf(f, "%s", el->class);
  if (sep == ',') fputc('"',f);
  fputc(sep,f);
  if (sep == ',') fputc('"',f);
  fprintf(f, "%s", el->valid);
  if (sep == ',') fputc('"',f);
  fputc(sep,f);
  fprintf(f, "%g", el->avHet);
  fputc(sep,f);
  fprintf(f, "%g", el->avHetSE);
  fputc(sep,f);
  if (sep == ',') fputc('"',f);
  fprintf(f, "%s", el->func);
  if (sep == ',') fputc('"',f);
  fputc(sep,f);
  if (sep == ',') fputc('"',f);
  fprintf(f, "%s", el->locType);
  if (sep == ',') fputc('"',f);
  fputc(sep,f);
  fprintf(f, "%u", el->weight);
  fputc(lastSep,f);
  }
  
  /* -------------------------------- End autoSql Generated Code -------------------------------- */
  
  
  void snp125TableCreate(struct sqlConnection *conn, char *tableName)
  /* create a snp125 table */
  {
  char *createString =
  "CREATE TABLE %s (\n"
  "    bin           smallint(5) unsigned not null,\n"
  "    chrom         varchar(15) not null,\n"
  "    chromStart    int(10) unsigned not null,\n"
  "    chromEnd      int(10) unsigned not null,\n"
  "    name          varchar(15) not null,\n"
  "    score         smallint(5) unsigned not null,\n"
  "    strand        enum('?','+','-') default '?' not null,\n"
  "    refNCBI       blob not null,\n"
  "    refUCSC       blob not null,\n"
  "    observed      varchar(255) not null,\n"
  "    molType       enum('unknown', 'genomic', 'cDNA') DEFAULT 'unknown' not null,\n"
  "    class         enum('unknown', 'single', 'in-del', 'het', 'microsatellite',"
  "                  'named', 'no var', 'mixed', 'mnp', 'insertion', 'deletion') \n"
  "                  DEFAULT 'unknown' NOT NULL,\n"
  "    valid         set('unknown', 'by-frequency', 'by-cluster', 'by-submitter', \n"
  "                  'by-2hit-2allele', 'by-hapmap') \n"
  "                  DEFAULT 'unknown' NOT NULL,\n"
  "    avHet 	   float not null,\n"
  "    avHetSE 	   float not null,\n"
  "    func          set( 'unknown', 'locus', 'coding', 'coding-synon', 'coding-nonsynon', \n"
  "                  'untranslated', 'intron','splice-site', 'cds-reference') \n"
  "                  DEFAULT 'unknown' NOT NULL,\n"
  "    locType       enum ('unknown', 'range', 'exact', 'between',\n"
  "                  'rangeInsertion', 'rangeSubstitution', 'rangeDeletion') DEFAULT 'unknown' NOT NULL\n,"
  "    weight        int not null\n"
  ")\n";
  
  struct dyString *dy = newDyString(1024);
  sqlDyStringPrintf(dy, createString, tableName);
  sqlRemakeTable(conn, tableName, dy->string);
  dyStringFree(&dy);
  }
  
  int snp125Cmp(const void *va, const void *vb)
  {
  const struct snp125 *a = *((struct snp125 **)va);
  const struct snp125 *b = *((struct snp125 **)vb);
  int dif;
  dif = strcmp(a->chrom, b->chrom);
  if (dif == 0)
      dif = a->chromStart - b->chromStart;
  return dif;
  }
  
  
  /*  Additional function for extended processing */
  
  
  struct snp125Extended *snpExtendedLoad(char **row)
  /* Load a snp125 from row fetched with select * from snp125
   * from database.  Additional fields are for run-time calculations */
  {
  struct snp125Extended *ret;
  
  AllocVar(ret);
  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]);
  ret->strand = cloneString(row[5]);
  ret->observed = cloneString(row[6]);
  ret->molType = cloneString(row[7]);
  ret->class = cloneString(row[8]);
  ret->valid = cloneString(row[9]);
  ret->avHet = atof(row[10]);
  ret->avHetSE = atof(row[11]);
  ret->func = cloneString(row[12]);
  ret->locType = cloneString(row[13]);
  ret->refNCBI = NULL;
  ret->refUCSC = NULL;
  ret->weight = 0;
  ret->nameExtra = cloneString("");
  ret->color = 0;
  
  return ret;
  }
  
  int snpVersion(char *track)
  /* If track starts with snpNNN where NNN is 125 or later, return the number;
   * otherwise return 0. */
  {
  int version = 0;
  if ( startsWith("snp", track) && strlen(track) >= 6 &&
       isdigit(track[3]) && isdigit(track[4]) && isdigit(track[5]) &&
       atoi(track+3) >= 125 )
      version = atoi(track+3);
  return version;
  }
  
  