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/liftOverChain.c src/hg/lib/liftOverChain.c
index d78ba6c..65b63be 100644
--- src/hg/lib/liftOverChain.c
+++ src/hg/lib/liftOverChain.c
@@ -1,223 +1,226 @@
 /* liftOverChain.c was originally generated by the autoSql program, which also 
  * generated liftOverChain.h and liftOverChain.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 "liftOverChain.h"
 
 
 void liftOverChainStaticLoad(char **row, struct liftOverChain *ret)
 /* Load a row from liftOverChain table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->fromDb = row[0];
 ret->toDb = row[1];
 ret->path = row[2];
 ret->minMatch = atof(row[3]);
 ret->minChainT = sqlUnsigned(row[4]);
 ret->minSizeQ = sqlUnsigned(row[5]);
 strcpy(ret->multiple, row[6]);
 ret->minBlocks = atof(row[7]);
 strcpy(ret->fudgeThick, row[8]);
 }
 
 struct liftOverChain *liftOverChainLoad(char **row)
 /* Load a liftOverChain from row fetched with select * from liftOverChain
  * from database.  Dispose of this with liftOverChainFree(). */
 {
 struct liftOverChain *ret;
 
 AllocVar(ret);
 ret->fromDb = cloneString(row[0]);
 ret->toDb = cloneString(row[1]);
 ret->path = cloneString(row[2]);
 ret->minMatch = atof(row[3]);
 ret->minChainT = sqlUnsigned(row[4]);
 ret->minSizeQ = sqlUnsigned(row[5]);
 strcpy(ret->multiple, row[6]);
 ret->minBlocks = atof(row[7]);
 strcpy(ret->fudgeThick, row[8]);
 return ret;
 }
 
 struct liftOverChain *liftOverChainLoadAll(char *fileName) 
 /* Load all liftOverChain from a whitespace-separated file.
  * Dispose of this with liftOverChainFreeList(). */
 {
 struct liftOverChain *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[9];
 
 while (lineFileRow(lf, row))
     {
     el = liftOverChainLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct liftOverChain *liftOverChainLoadAllByChar(char *fileName, char chopper) 
 /* Load all liftOverChain from a chopper separated file.
  * Dispose of this with liftOverChainFreeList(). */
 {
 struct liftOverChain *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[9];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = liftOverChainLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct liftOverChain *liftOverChainLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all liftOverChain from table that satisfy the query given.  
  * Where query is of the form 'select * from example where something=something'
  * or 'select example.* from example, anotherTable where example.something = 
  * anotherTable.something'.
  * Dispose of this with liftOverChainFreeList(). */
 {
 struct liftOverChain *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = liftOverChainLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void liftOverChainSaveToDb(struct sqlConnection *conn, struct liftOverChain *el, char *tableName, int updateSize)
 /* Save liftOverChain as a row to the table specified by tableName. 
  * As blob fields may be arbitrary size updateSize specifies the approx size
  * of a string that would contain the entire query. Arrays of native types are
  * converted to comma separated strings and loaded as such, User defined types are
  * inserted as NULL. Strings are automatically escaped to allow insertion into the database. */
 {
 struct dyString *update = newDyString(updateSize);
 sqlDyStringPrintf(update, "insert into %s values ( '%s','%s','%s',%g,%u,%u,'%s',%g,'%s')", 
 	tableName,  el->fromDb,  el->toDb,  el->path,  el->minMatch,  el->minChainT,  el->minSizeQ,  el->multiple,  el->minBlocks,  el->fudgeThick);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
 
 struct liftOverChain *liftOverChainCommaIn(char **pS, struct liftOverChain *ret)
 /* Create a liftOverChain out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new liftOverChain */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->fromDb = sqlStringComma(&s);
 ret->toDb = sqlStringComma(&s);
 ret->path = sqlStringComma(&s);
 ret->minMatch = sqlFloatComma(&s);
 ret->minChainT = sqlUnsignedComma(&s);
 ret->minSizeQ = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, ret->multiple, sizeof(ret->multiple));
 ret->minBlocks = sqlFloatComma(&s);
 sqlFixedStringComma(&s, ret->fudgeThick, sizeof(ret->fudgeThick));
 *pS = s;
 return ret;
 }
 
 void liftOverChainFree(struct liftOverChain **pEl)
 /* Free a single dynamically allocated liftOverChain such as created
  * with liftOverChainLoad(). */
 {
 struct liftOverChain *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->fromDb);
 freeMem(el->toDb);
 freeMem(el->path);
 freez(pEl);
 }
 
 void liftOverChainFreeList(struct liftOverChain **pList)
 /* Free a list of dynamically allocated liftOverChain's */
 {
 struct liftOverChain *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     liftOverChainFree(&el);
     }
 *pList = NULL;
 }
 
 void liftOverChainOutput(struct liftOverChain *el, FILE *f, char sep, char lastSep) 
 /* Print out liftOverChain.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->fromDb);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->toDb);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->path);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%g", el->minMatch);
 fputc(sep,f);
 fprintf(f, "%u", el->minChainT);
 fputc(sep,f);
 fprintf(f, "%u", el->minSizeQ);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->multiple);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%g", el->minBlocks);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->fudgeThick);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 boolean liftOverChainExists(struct sqlConnection *conn, char *tableName,
                                 char *fromDb, char *toDb)
 /* Return TRUE if row where fromDb and toDb match */
 {
 char query[256];
 sqlSafef(query, sizeof(query), 
         "select count(*) from %s where fromDb = '%s' and toDb = '%s'",
 	        tableName, fromDb, toDb);
 return sqlQuickNum(conn, query) > 0;
 }
 
 void liftOverChainRemove(struct sqlConnection *conn, char *tableName,
                                 char *fromDb, char *toDb)
 /* Remove rows where fromDb and toDb match */
 {
 char query[256];
 sqlSafef(query, sizeof(query), 
         "delete from %s where fromDb = '%s' and toDb = '%s'",
 	        tableName, fromDb, toDb);
 sqlUpdate(conn, query);
 }