text: /* bedDetail.c was originally generated by the autoSql program, which also
   * generated bedDetail.h and bedDetail.sql.  This module links the database and
   * the RAM representation of objects. */
  
  /* Copyright (C) 2014 The Regents of the University of California 
   * See README in this or parent directory for licensing information. */
  
  #include "common.h"
  #include "linefile.h"
  #include "dystring.h"
  #include "jksql.h"
  #include "basicBed.h"
  #include "bedDetail.h"
  
  
  struct bedDetail *bedDetailLoad(char **row)
  /* Load a bedDetail from row fetched with select * from bedDetail
   * from database.  Dispose of this with bedDetailFree(). */
  {
  struct bedDetail *ret;
  
  AllocVar(ret);
  ret->blockCount = sqlSigned(row[9]);
  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]);
  safecpy(ret->strand, sizeof(ret->strand), row[5]);
  ret->thickStart = sqlUnsigned(row[6]);
  ret->thickEnd = sqlUnsigned(row[7]);
  ret->reserved = sqlUnsigned(row[8]);
  {
  int sizeOne;
  sqlSignedDynamicArray(row[10], &ret->blockSizes, &sizeOne);
  assert(sizeOne == ret->blockCount);
  }
  {
  int sizeOne;
  sqlSignedDynamicArray(row[11], &ret->chromStarts, &sizeOne);
  assert(sizeOne == ret->blockCount);
  }
  ret->id = cloneString(row[12]);
  ret->description = cloneString(row[13]);
  return ret;
  }
  
  struct bedDetail *bedDetailLoadAll(char *fileName)
  /* Load all bedDetail from a whitespace-separated file.
   * Dispose of this with bedDetailFreeList(). */
  {
  struct bedDetail *list = NULL, *el;
  struct lineFile *lf = lineFileOpen(fileName, TRUE);
  char *row[14];
  
  while (lineFileRow(lf, row))
      {
      el = bedDetailLoad(row);
      slAddHead(&list, el);
      }
  lineFileClose(&lf);
  slReverse(&list);
  return list;
  }
  
  struct bedDetail *bedDetailLoadAllByChar(char *fileName, char chopper)
  /* Load all bedDetail from a chopper separated file.
   * Dispose of this with bedDetailFreeList(). */
  {
  struct bedDetail *list = NULL, *el;
  struct lineFile *lf = lineFileOpen(fileName, TRUE);
  char *row[14];
  
  while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
      {
      el = bedDetailLoad(row);
      slAddHead(&list, el);
      }
  lineFileClose(&lf);
  slReverse(&list);
  return list;
  }
  
  struct bedDetail *bedDetailCommaIn(char **pS, struct bedDetail *ret)
  /* Create a bedDetail out of a comma separated string.
   * This will fill in ret if non-null, otherwise will
   * return a new bedDetail */
  {
  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);
  sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
  ret->thickStart = sqlUnsignedComma(&s);
  ret->thickEnd = sqlUnsignedComma(&s);
  ret->reserved = sqlUnsignedComma(&s);
  ret->blockCount = sqlSignedComma(&s);
  {
  int i;
  s = sqlEatChar(s, '{');
  AllocArray(ret->blockSizes, ret->blockCount);
  for (i=0; i<ret->blockCount; ++i)
      {
      ret->blockSizes[i] = sqlSignedComma(&s);
      }
  s = sqlEatChar(s, '}');
  s = sqlEatChar(s, ',');
  }
  {
  int i;
  s = sqlEatChar(s, '{');
  AllocArray(ret->chromStarts, ret->blockCount);
  for (i=0; i<ret->blockCount; ++i)
      {
      ret->chromStarts[i] = sqlSignedComma(&s);
      }
  s = sqlEatChar(s, '}');
  s = sqlEatChar(s, ',');
  }
  ret->id = sqlStringComma(&s);
  ret->description = sqlStringComma(&s);
  *pS = s;
  return ret;
  }
  
  void bedDetailFree(struct bedDetail **pEl)
  /* Free a single dynamically allocated bedDetail such as created
   * with bedDetailLoad(). */
  {
  struct bedDetail *el;
  
  if ((el = *pEl) == NULL) return;
  freeMem(el->chrom);
  freeMem(el->name);
  freeMem(el->blockSizes);
  freeMem(el->chromStarts);
  freeMem(el->id);
  freeMem(el->description);
  freez(pEl);
  }
  
  void bedDetailFreeList(struct bedDetail **pList)
  /* Free a list of dynamically allocated bedDetail's */
  {
  struct bedDetail *el, *next;
  
  for (el = *pList; el != NULL; el = next)
      {
      next = el->next;
      bedDetailFree(&el);
      }
  *pList = NULL;
  }
  
  void bedDetailOutput(struct bedDetail *el, FILE *f, char sep, char lastSep, int size)
  /* Print out bedDetail.  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);
  if (size > 6)
      {
      fprintf(f, "%u", el->score);
      fputc(sep,f);
      }
  if (size > 7)
      {
      if (sep == ',') fputc('"',f);
      fprintf(f, "%s", el->strand);
      if (sep == ',') fputc('"',f);
      fputc(sep,f);
      }
  if (size > 8)
      {
      fprintf(f, "%u", el->thickStart);
      fputc(sep,f);
      }
  if (size > 9)
      {
      fprintf(f, "%u", el->thickEnd);
      fputc(sep,f);
      }
  if (size > 10)
      {
      fprintf(f, "%u", el->reserved);
      fputc(sep,f);
      }
  if (size > 11)
      {
      fprintf(f, "%d", el->blockCount);
      fputc(sep,f);
      }
  if (size > 12)
      {
      int i;
      if (sep == ',') fputc('{',f);
      for (i=0; i<el->blockCount; ++i)
          {
          fprintf(f, "%d", el->blockSizes[i]);
          fputc(',', f);
          }
      if (sep == ',') fputc('}',f);
      fputc(sep,f);
      }
  if (size > 13)
      {
      int i;
      if (sep == ',') fputc('{',f);
      for (i=0; i<el->blockCount; ++i)
          {
          fprintf(f, "%d", el->chromStarts[i]);
          fputc(',', f);
          }
      if (sep == ',') fputc('}',f);
      fputc(sep,f);
      }
  /* last 2 should always be present */
  if (sep == ',') fputc('"',f);
  fprintf(f, "%s", el->id);
  if (sep == ',') fputc('"',f);
  fputc(sep,f);
  if (sep == ',') fputc('"',f);
  fprintf(f, "%s", el->description);
  if (sep == ',') fputc('"',f);
  fputc(lastSep,f);
  }
  
  /* -------------------------------- End autoSql Generated Code -------------------------------- */
  
  static char *bedDetailAutoSqlString =
  "table bedDetail\n"
  "\"Browser extensible data, with extended fields for detail page\"\n"
  "   (\n"
  "   string chrom;      \"Reference sequence chromosome or scaffold\"\n"
  "   uint   chromStart; \"Start position in chromosome\"\n"
  "   uint   chromEnd;   \"End position in chromosome\"\n"
  "   string name;       \"Short Name of item\"\n"
  "   uint   score;      \"Score from 0-1000\"\n"
  "   char[1] strand;    \"+ or -\"\n"
  "   uint thickStart;   \"Start of where display should be thick (start codon)\"\n"
  "   uint thickEnd;     \"End of where display should be thick (stop codon)\"\n"
  "   uint reserved;     \"Used as itemRgb as of 2004-11-22\"\n"
  "   int blockCount;    \"Number of blocks\"\n"
  "   int[blockCount] blockSizes; \"Comma separated list of block sizes\"\n"
  "   int[blockCount] chromStarts; \"Start positions relative to chromStart\"\n"
  "   string id;         \"ID to bed used in URL to link back\"\n"
  "   lstring description; \"Long description of item for the details page\"\n"
  "   )\n"
  ;
  
  struct asObject *bedDetailAsObj()
  // Return asObject describing fields of bedDetail
  {
  return asParseText(bedDetailAutoSqlString);
  }
  
  struct bedDetail *bedDetailLoadWithGaps(char **row, int size)
  /* Load a bedDetail from row split from a file or from database,
     may have parts of BED not included.  Dispose of this with bedDetailFree().
     Size is total number of fields
  */
  {
  struct bedDetail *ret;
  AllocVar(ret);
  ret->chrom = cloneString(row[0]);
  ret->chromStart = sqlUnsigned(row[1]);
  ret->chromEnd = sqlUnsigned(row[2]);
  ret->name = cloneString(row[3]);
  if (size > 6 && row[4] != NULL)
      ret->score = sqlUnsigned(row[4]);
  if (size > 7 && row[5] != NULL)
      safecpy(ret->strand, sizeof(ret->strand), row[5]);
  if (size > 8 && row[6] != NULL)
      ret->thickStart = sqlUnsigned(row[6]);
  if (size > 9 && row[7] != NULL)
      ret->thickEnd = sqlUnsigned(row[7]);
  if (size > 10 && row[8] != NULL)
      {
      char *comma = strchr(row[8], ',');
      if (comma)
          ret->reserved = bedParseRgb(row[8]);
      else
          ret->reserved = 0;
      }
  if (size > 11 && row[9] != NULL)
      ret->blockCount = sqlSigned(row[9]);
  if (size > 12 && row[10] != NULL)
      {
      int sizeOne;
      sqlSignedDynamicArray(row[10], &ret->blockSizes, &sizeOne);
      assert(sizeOne == ret->blockCount);
      }
  if (size > 13 && row[11] != NULL)
      {
      int sizeOne;
      sqlSignedDynamicArray(row[11], &ret->chromStarts, &sizeOne);
      assert(sizeOne == ret->blockCount);
      }
  /* these 2 should not be null, but always last 2 */
  ret->id = cloneString(row[size-2]);
  ret->description = cloneString(row[size-1]);
  return ret;
  }
  
  struct bedDetail *bedDetailLineFileLoad (char **row, int size, struct lineFile *lf)
  /* load from linefile line, with error checking */
  {
  struct bedDetail *item;
  int count; /* block count */
  int wordCount = size - 2; /* bed part of row */
  AllocVar(item);
  item->chrom = cloneString(row[0]);
  item->chromStart = lineFileNeedNum(lf, row, 1);
  item->chromEnd = lineFileNeedNum(lf, row, 2);
  if (item->chromEnd < 1)
      lineFileAbort(lf, "chromEnd less than 1 (%d)", item->chromEnd);
  if (item->chromEnd < item->chromStart)
      lineFileAbort(lf, "chromStart after chromEnd (%d > %d)",
          item->chromStart, item->chromEnd);
  if (wordCount > 3)
       item->name = cloneString(row[3]);
  if (wordCount > 4)
       item->score = lineFileNeedNum(lf, row, 4);
  if (wordCount > 5)
       {
       strncpy(item->strand, row[5], sizeof(item->strand));
       if (item->strand[0] != '+' && item->strand[0] != '-' && item->strand[0] != '.')
            lineFileAbort(lf, "Expecting + or - in strand");
       }
  if (wordCount > 6)
       item->thickStart = lineFileNeedNum(lf, row, 6);
  else
       item->thickStart = item->chromStart;
  if (wordCount > 7)
       {
       item->thickEnd = lineFileNeedNum(lf, row, 7);
       if (item->thickEnd < item->thickStart)
           lineFileAbort(lf, "thickStart after thickEnd");
       if ((item->thickStart != 0) &&
           ((item->thickStart < item->chromStart) ||
            (item->thickStart > item->chromEnd)))
           lineFileAbort(lf,
               "thickStart out of range (chromStart to chromEnd, or 0 if no CDS)");
       if ((item->thickEnd != 0) &&
           ((item->thickEnd < item->chromStart) ||
            (item->thickEnd > item->chromEnd)))
           lineFileAbort(lf,
               "thickEnd out of range for %s:%d-%d, thick:%d-%d (chromStart to chromEnd, or 0 if no CDS)",
                         item->name, item->chromStart, item->chromEnd,
                         item->thickStart, item->thickEnd);
       }
  else
       item->thickEnd = item->chromEnd;
  if (wordCount > 8)
      {
      char *comma;
      /*  Allow comma separated list of rgb values here   */
      comma = strchr(row[8], ',');
      if (comma)
          {
          int rgb = bedParseRgb(row[8]);
          if (rgb < 0)
              lineFileAbort(lf,
                  "Expecting 3 comma separated numbers for r,g,b bed item color.");
          else
              item->reserved = rgb;
          }
      else
          item->reserved = lineFileNeedNum(lf, row, 8);
      }
  if (wordCount > 9)
      item->blockCount = lineFileNeedNum(lf, row, 9);
  if (wordCount > 10)
      {
      sqlSignedDynamicArray(row[10], &item->blockSizes, &count);
      if (count != item->blockCount)
          lineFileAbort(lf,  "expecting %d elements in array", item->blockCount);
      }
  if (wordCount > 11)
      {
      int i;
      sqlSignedDynamicArray(row[11], &item->chromStarts, &count);
      if (count != item->blockCount)
          lineFileAbort(lf, "expecting %d elements in array", item->blockCount);
      // tell the user if they appear to be using absolute starts rather than
      // relative... easy to forget!  Also check block order, coord ranges...
      for (i=0;  i < item->blockCount;  i++)
          {
          if (item->chromStarts[i]+item->chromStart >= item->chromEnd)
              {
              if (item->chromStarts[i] >= item->chromStart)
                  lineFileAbort(lf,
                      "BED chromStarts offsets must be relative to chromStart, "
                      "not absolute.  Try subtracting chromStart from each offset "
                      "in chromStarts.");
              else
                  lineFileAbort(lf,
                      "BED chromStarts[i]+chromStart must be less than chromEnd.");
              }
          }
      if (item->chromStarts[0] != 0)
          lineFileAbort(lf,
              "BED blocks must span chromStart to chromEnd.  "
              "BED chromStarts[0] must be 0 (==%d) so that (chromStart + "
              "chromStarts[0]) equals chromStart.", item->chromStarts[0]);
      i = item->blockCount-1;
      if ((item->chromStart + item->chromStarts[i] + item->blockSizes[i]) !=
          item->chromEnd)
          {
          lineFileAbort(lf,
              "BED blocks must span chromStart to chromEnd.  (chromStart + "
              "chromStarts[last] + blockSizes[last]) must equal chromEnd.");
          }
      }
      /* these 2 should not be null (maybe empty string), but always last 2 */
      item->id = cloneString(row[size-2]);
      item->description = cloneString(row[size-1]);
  return item;
  }
  
  