e85899748df910ff2759e5b7f7affda61e5905d1
braney
  Wed Apr 8 11:28:08 2015 -0700
a few more files used for little feet mode

diff --git src/hg/lib/adjacency.c src/hg/lib/adjacency.c
new file mode 100644
index 0000000..c6eaaa0
--- /dev/null
+++ src/hg/lib/adjacency.c
@@ -0,0 +1,168 @@
+/* adjacency.c was originally generated by the autoSql program, which also 
+ * generated adjacency.h and adjacency.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 "adjacency.h"
+
+
+
+char *adjacencyCommaSepFieldNames = "chrom,chromStart,chromEnd,name,score,strand1,strand2,cycle,ordering";
+
+void adjacencyStaticLoad(char **row, struct adjacency *ret)
+/* Load a row from adjacency 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]);
+safecpy(ret->strand1, sizeof(ret->strand1), row[5]);
+safecpy(ret->strand2, sizeof(ret->strand2), row[6]);
+ret->cycle = row[7];
+ret->ordering = sqlUnsigned(row[8]);
+}
+
+struct adjacency *adjacencyLoad(char **row)
+/* Load a adjacency from row fetched with select * from adjacency
+ * from database.  Dispose of this with adjacencyFree(). */
+{
+struct adjacency *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]);
+safecpy(ret->strand1, sizeof(ret->strand1), row[5]);
+safecpy(ret->strand2, sizeof(ret->strand2), row[6]);
+ret->cycle = cloneString(row[7]);
+ret->ordering = sqlUnsigned(row[8]);
+return ret;
+}
+
+struct adjacency *adjacencyLoadAll(char *fileName) 
+/* Load all adjacency from a whitespace-separated file.
+ * Dispose of this with adjacencyFreeList(). */
+{
+struct adjacency *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[9];
+
+while (lineFileRow(lf, row))
+    {
+    el = adjacencyLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct adjacency *adjacencyLoadAllByChar(char *fileName, char chopper) 
+/* Load all adjacency from a chopper separated file.
+ * Dispose of this with adjacencyFreeList(). */
+{
+struct adjacency *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[9];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = adjacencyLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct adjacency *adjacencyCommaIn(char **pS, struct adjacency *ret)
+/* Create a adjacency out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new adjacency */
+{
+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->strand1, sizeof(ret->strand1));
+sqlFixedStringComma(&s, ret->strand2, sizeof(ret->strand2));
+ret->cycle = sqlStringComma(&s);
+ret->ordering = sqlUnsignedComma(&s);
+*pS = s;
+return ret;
+}
+
+void adjacencyFree(struct adjacency **pEl)
+/* Free a single dynamically allocated adjacency such as created
+ * with adjacencyLoad(). */
+{
+struct adjacency *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->chrom);
+freeMem(el->name);
+freeMem(el->cycle);
+freez(pEl);
+}
+
+void adjacencyFreeList(struct adjacency **pList)
+/* Free a list of dynamically allocated adjacency's */
+{
+struct adjacency *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    adjacencyFree(&el);
+    }
+*pList = NULL;
+}
+
+void adjacencyOutput(struct adjacency *el, FILE *f, char sep, char lastSep) 
+/* Print out adjacency.  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->strand1);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->strand2);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->cycle);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%u", el->ordering);
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+