src/hg/lib/hapmapPhaseIIISummary.c 1.1

Index: src/hg/lib/hapmapPhaseIIISummary.c
===================================================================
RCS file: src/hg/lib/hapmapPhaseIIISummary.c
diff -N src/hg/lib/hapmapPhaseIIISummary.c
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/hg/lib/hapmapPhaseIIISummary.c	6 Mar 2009 23:34:41 -0000	1.1
@@ -0,0 +1,272 @@
+/* hapmapPhaseIIISummary.c was originally generated by the autoSql program, which also 
+ * generated hapmapPhaseIIISummary.h and hapmapPhaseIIISummary.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 "hapmapPhaseIIISummary.h"
+
+static char const rcsid[] = "$Id$";
+
+struct hapmapPhaseIIISummary *hapmapPhaseIIISummaryLoad(char **row)
+/* Load a hapmapPhaseIIISummary from row fetched with select * from hapmapPhaseIIISummary
+ * from database.  Dispose of this with hapmapPhaseIIISummaryFree(). */
+{
+struct hapmapPhaseIIISummary *ret;
+
+AllocVar(ret);
+ret->orthoCount = sqlUnsigned(row[15]);
+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->observed = cloneString(row[5]);
+ret->overallMajorAllele = row[6][0];
+ret->overallMinorAllele = row[7][0];
+ret->popCount = sqlUnsigned(row[8]);
+ret->phaseIIPopCount = sqlUnsigned(row[9]);
+ret->isMixed = sqlUnsigned(row[10]);
+sqlUbyteArray(row[11], ret->foundInPop, 11);
+sqlUbyteArray(row[12], ret->monomorphicInPop, 11);
+ret->minFreq = sqlFloat(row[13]);
+ret->maxFreq = sqlFloat(row[14]);
+{
+int sizeOne;
+sqlCharDynamicArray(row[16], &ret->orthoAlleles, &sizeOne);
+assert(sizeOne == ret->orthoCount);
+}
+{
+int sizeOne;
+sqlUshortDynamicArray(row[17], &ret->orthoQuals, &sizeOne);
+assert(sizeOne == ret->orthoCount);
+}
+return ret;
+}
+
+struct hapmapPhaseIIISummary *hapmapPhaseIIISummaryLoadAll(char *fileName) 
+/* Load all hapmapPhaseIIISummary from a whitespace-separated file.
+ * Dispose of this with hapmapPhaseIIISummaryFreeList(). */
+{
+struct hapmapPhaseIIISummary *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[18];
+
+while (lineFileRow(lf, row))
+    {
+    el = hapmapPhaseIIISummaryLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct hapmapPhaseIIISummary *hapmapPhaseIIISummaryLoadAllByChar(char *fileName, char chopper) 
+/* Load all hapmapPhaseIIISummary from a chopper separated file.
+ * Dispose of this with hapmapPhaseIIISummaryFreeList(). */
+{
+struct hapmapPhaseIIISummary *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[18];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = hapmapPhaseIIISummaryLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct hapmapPhaseIIISummary *hapmapPhaseIIISummaryCommaIn(char **pS, struct hapmapPhaseIIISummary *ret)
+/* Create a hapmapPhaseIIISummary out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new hapmapPhaseIIISummary */
+{
+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->observed = sqlStringComma(&s);
+sqlFixedStringComma(&s, &(ret->overallMajorAllele), sizeof(ret->overallMajorAllele));
+sqlFixedStringComma(&s, &(ret->overallMinorAllele), sizeof(ret->overallMinorAllele));
+ret->popCount = sqlUnsignedComma(&s);
+ret->phaseIIPopCount = sqlUnsignedComma(&s);
+ret->isMixed = sqlUnsignedComma(&s);
+{
+int i;
+s = sqlEatChar(s, '{');
+for (i=0; i<11; ++i)
+    {
+    ret->foundInPop[i] = sqlUnsignedComma(&s);
+    }
+s = sqlEatChar(s, '}');
+s = sqlEatChar(s, ',');
+}
+{
+int i;
+s = sqlEatChar(s, '{');
+for (i=0; i<11; ++i)
+    {
+    ret->monomorphicInPop[i] = sqlUnsignedComma(&s);
+    }
+s = sqlEatChar(s, '}');
+s = sqlEatChar(s, ',');
+}
+ret->minFreq = sqlFloatComma(&s);
+ret->maxFreq = sqlFloatComma(&s);
+ret->orthoCount = sqlUnsignedComma(&s);
+{
+int i;
+s = sqlEatChar(s, '{');
+AllocArray(ret->orthoAlleles, ret->orthoCount);
+for (i=0; i<ret->orthoCount; ++i)
+    {
+    ret->orthoAlleles[i] = sqlCharComma(&s);
+    }
+s = sqlEatChar(s, '}');
+s = sqlEatChar(s, ',');
+}
+{
+int i;
+s = sqlEatChar(s, '{');
+AllocArray(ret->orthoQuals, ret->orthoCount);
+for (i=0; i<ret->orthoCount; ++i)
+    {
+    ret->orthoQuals[i] = sqlUnsignedComma(&s);
+    }
+s = sqlEatChar(s, '}');
+s = sqlEatChar(s, ',');
+}
+*pS = s;
+return ret;
+}
+
+void hapmapPhaseIIISummaryFree(struct hapmapPhaseIIISummary **pEl)
+/* Free a single dynamically allocated hapmapPhaseIIISummary such as created
+ * with hapmapPhaseIIISummaryLoad(). */
+{
+struct hapmapPhaseIIISummary *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->chrom);
+freeMem(el->name);
+freeMem(el->observed);
+freeMem(el->orthoAlleles);
+freeMem(el->orthoQuals);
+freez(pEl);
+}
+
+void hapmapPhaseIIISummaryFreeList(struct hapmapPhaseIIISummary **pList)
+/* Free a list of dynamically allocated hapmapPhaseIIISummary's */
+{
+struct hapmapPhaseIIISummary *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    hapmapPhaseIIISummaryFree(&el);
+    }
+*pList = NULL;
+}
+
+void hapmapPhaseIIISummaryOutput(struct hapmapPhaseIIISummary *el, FILE *f, char sep, char lastSep) 
+/* Print out hapmapPhaseIIISummary.  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->observed);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%c", el->overallMajorAllele);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%c", el->overallMinorAllele);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%u", el->popCount);
+fputc(sep,f);
+fprintf(f, "%u", el->phaseIIPopCount);
+fputc(sep,f);
+fprintf(f, "%u", el->isMixed);
+fputc(sep,f);
+{
+int i;
+if (sep == ',') fputc('{',f);
+for (i=0; i<11; ++i)
+    {
+    fprintf(f, "%u", el->foundInPop[i]);
+    fputc(',', f);
+    }
+if (sep == ',') fputc('}',f);
+}
+fputc(sep,f);
+{
+int i;
+if (sep == ',') fputc('{',f);
+for (i=0; i<11; ++i)
+    {
+    fprintf(f, "%u", el->monomorphicInPop[i]);
+    fputc(',', f);
+    }
+if (sep == ',') fputc('}',f);
+}
+fputc(sep,f);
+fprintf(f, "%g", el->minFreq);
+fputc(sep,f);
+fprintf(f, "%g", el->maxFreq);
+fputc(sep,f);
+fprintf(f, "%u", el->orthoCount);
+fputc(sep,f);
+{
+int i;
+if (sep == ',') fputc('{',f);
+for (i=0; i<el->orthoCount; ++i)
+    {
+    if (sep == ',') fputc('"',f);
+    fprintf(f, "%c", el->orthoAlleles[i]);
+    if (sep == ',') fputc('"',f);
+    fputc(',', f);
+    }
+if (sep == ',') fputc('}',f);
+}
+fputc(sep,f);
+{
+int i;
+if (sep == ',') fputc('{',f);
+for (i=0; i<el->orthoCount; ++i)
+    {
+    fprintf(f, "%u", el->orthoQuals[i]);
+    fputc(',', f);
+    }
+if (sep == ',') fputc('}',f);
+}
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+