e70152e44cc66cc599ff6b699eb8adc07f3e656a
kent
  Sat May 24 21:09:34 2014 -0700
Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
diff --git src/hg/lib/syntenySanger.c src/hg/lib/syntenySanger.c
index c950f60..eb49b80 100644
--- src/hg/lib/syntenySanger.c
+++ src/hg/lib/syntenySanger.c
@@ -1,150 +1,153 @@
 /* syntenySanger.c was originally generated by the autoSql program, which also 
  * generated syntenySanger.h and syntenySanger.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 "syntenySanger.h"
 
 
 void syntenySangerStaticLoad(char **row, struct syntenySanger *ret)
 /* Load a row from syntenySanger 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]);
 strcpy(ret->strand, row[5]);
 }
 
 struct syntenySanger *syntenySangerLoad(char **row)
 /* Load a syntenySanger from row fetched with select * from syntenySanger
  * from database.  Dispose of this with syntenySangerFree(). */
 {
 struct syntenySanger *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]);
 strcpy(ret->strand, row[5]);
 return ret;
 }
 
 struct syntenySanger *syntenySangerLoadAll(char *fileName) 
 /* Load all syntenySanger from a tab-separated file.
  * Dispose of this with syntenySangerFreeList(). */
 {
 struct syntenySanger *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[6];
 
 while (lineFileRow(lf, row))
     {
     el = syntenySangerLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct syntenySanger *syntenySangerLoadWhere(struct sqlConnection *conn, char *table, char *where)
 /* Load all syntenySanger from table that satisfy where clause. The
  * where clause may be NULL in which case whole table is loaded
  * Dispose of this with syntenySangerFreeList(). */
 {
 struct syntenySanger *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 = syntenySangerLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 dyStringFree(&query);
 return list;
 }
 
 struct syntenySanger *syntenySangerCommaIn(char **pS, struct syntenySanger *ret)
 /* Create a syntenySanger out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new syntenySanger */
 {
 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));
 *pS = s;
 return ret;
 }
 
 void syntenySangerFree(struct syntenySanger **pEl)
 /* Free a single dynamically allocated syntenySanger such as created
  * with syntenySangerLoad(). */
 {
 struct syntenySanger *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freez(pEl);
 }
 
 void syntenySangerFreeList(struct syntenySanger **pList)
 /* Free a list of dynamically allocated syntenySanger's */
 {
 struct syntenySanger *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     syntenySangerFree(&el);
     }
 *pList = NULL;
 }
 
 void syntenySangerOutput(struct syntenySanger *el, FILE *f, char sep, char lastSep) 
 /* Print out syntenySanger.  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(lastSep,f);
 }