533112afe2a2005e80cdb1f82904ea65032d4302
braney
  Sat Oct 2 11:37:34 2021 -0700
split hg/lib into two separate libaries, one only used by the cgis

diff --git src/hg/cgilib/simpleRepeat.c src/hg/cgilib/simpleRepeat.c
new file mode 100644
index 0000000..9893599
--- /dev/null
+++ src/hg/cgilib/simpleRepeat.c
@@ -0,0 +1,204 @@
+/* simpleRepeat.c was originally generated by the autoSql program, which also 
+ * generated simpleRepeat.h and simpleRepeat.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 "simpleRepeat.h"
+
+
+void simpleRepeatStaticLoad(char **row, struct simpleRepeat *ret)
+/* Load a row from simpleRepeat 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->period = sqlUnsigned(row[4]);
+ret->copyNum = atof(row[5]);
+ret->consensusSize = sqlUnsigned(row[6]);
+ret->perMatch = sqlUnsigned(row[7]);
+ret->perIndel = sqlUnsigned(row[8]);
+ret->score = sqlUnsigned(row[9]);
+ret->A = sqlUnsigned(row[10]);
+ret->C = sqlUnsigned(row[11]);
+ret->G = sqlUnsigned(row[12]);
+ret->T = sqlUnsigned(row[13]);
+ret->entropy = atof(row[14]);
+ret->sequence = row[15];
+}
+
+struct simpleRepeat *simpleRepeatLoad(char **row)
+/* Load a simpleRepeat from row fetched with select * from simpleRepeat
+ * from database.  Dispose of this with simpleRepeatFree(). */
+{
+struct simpleRepeat *ret;
+
+AllocVar(ret);
+ret->chrom = cloneString(row[0]);
+ret->chromStart = sqlUnsigned(row[1]);
+ret->chromEnd = sqlUnsigned(row[2]);
+ret->name = cloneString(row[3]);
+ret->period = sqlUnsigned(row[4]);
+ret->copyNum = atof(row[5]);
+ret->consensusSize = sqlUnsigned(row[6]);
+ret->perMatch = sqlUnsigned(row[7]);
+ret->perIndel = sqlUnsigned(row[8]);
+ret->score = sqlUnsigned(row[9]);
+ret->A = sqlUnsigned(row[10]);
+ret->C = sqlUnsigned(row[11]);
+ret->G = sqlUnsigned(row[12]);
+ret->T = sqlUnsigned(row[13]);
+ret->entropy = atof(row[14]);
+ret->sequence = cloneString(row[15]);
+return ret;
+}
+
+struct simpleRepeat *simpleRepeatLoadAll(char *fileName) 
+/* Load all simpleRepeat from a tab-separated file.
+ * Dispose of this with simpleRepeatFreeList(). */
+{
+struct simpleRepeat *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[16];
+
+while (lineFileRow(lf, row))
+    {
+    el = simpleRepeatLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct simpleRepeat *simpleRepeatLoadWhere(struct sqlConnection *conn, char *table, char *where)
+/* Load all simpleRepeat from table that satisfy where clause. The
+ * where clause may be NULL in which case whole table is loaded
+ * Dispose of this with simpleRepeatFreeList(). */
+{
+struct simpleRepeat *list = NULL, *el;
+struct dyString *query = dyStringNew(256);
+struct sqlResult *sr;
+char **row;
+
+sqlDyStringPrintf(query, "select * from %s", table);
+if (where != NULL)
+    dyStringPrintf(query, " where %s", where);
+sr = sqlGetResult(conn, query->string);
+while ((row = sqlNextRow(sr)) != NULL)
+    {
+    el = simpleRepeatLoad(row);
+    slAddHead(&list, el);
+    }
+slReverse(&list);
+sqlFreeResult(&sr);
+dyStringFree(&query);
+return list;
+}
+
+struct simpleRepeat *simpleRepeatCommaIn(char **pS, struct simpleRepeat *ret)
+/* Create a simpleRepeat out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new simpleRepeat */
+{
+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->period = sqlUnsignedComma(&s);
+ret->copyNum = sqlFloatComma(&s);
+ret->consensusSize = sqlUnsignedComma(&s);
+ret->perMatch = sqlUnsignedComma(&s);
+ret->perIndel = sqlUnsignedComma(&s);
+ret->score = sqlUnsignedComma(&s);
+ret->A = sqlUnsignedComma(&s);
+ret->C = sqlUnsignedComma(&s);
+ret->G = sqlUnsignedComma(&s);
+ret->T = sqlUnsignedComma(&s);
+ret->entropy = sqlFloatComma(&s);
+ret->sequence = sqlStringComma(&s);
+*pS = s;
+return ret;
+}
+
+void simpleRepeatFree(struct simpleRepeat **pEl)
+/* Free a single dynamically allocated simpleRepeat such as created
+ * with simpleRepeatLoad(). */
+{
+struct simpleRepeat *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->chrom);
+freeMem(el->name);
+freeMem(el->sequence);
+freez(pEl);
+}
+
+void simpleRepeatFreeList(struct simpleRepeat **pList)
+/* Free a list of dynamically allocated simpleRepeat's */
+{
+struct simpleRepeat *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    simpleRepeatFree(&el);
+    }
+*pList = NULL;
+}
+
+void simpleRepeatOutput(struct simpleRepeat *el, FILE *f, char sep, char lastSep) 
+/* Print out simpleRepeat.  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->period);
+fputc(sep,f);
+fprintf(f, "%f", el->copyNum);
+fputc(sep,f);
+fprintf(f, "%u", el->consensusSize);
+fputc(sep,f);
+fprintf(f, "%u", el->perMatch);
+fputc(sep,f);
+fprintf(f, "%u", el->perIndel);
+fputc(sep,f);
+fprintf(f, "%u", el->score);
+fputc(sep,f);
+fprintf(f, "%u", el->A);
+fputc(sep,f);
+fprintf(f, "%u", el->C);
+fputc(sep,f);
+fprintf(f, "%u", el->G);
+fputc(sep,f);
+fprintf(f, "%u", el->T);
+fputc(sep,f);
+fprintf(f, "%f", el->entropy);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->sequence);
+if (sep == ',') fputc('"',f);
+fputc(lastSep,f);
+}
+