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/hapmapPrimateAlleles.c src/hg/lib/hapmapPrimateAlleles.c
index 6f9148c..194fca3 100644
--- src/hg/lib/hapmapPrimateAlleles.c
+++ src/hg/lib/hapmapPrimateAlleles.c
@@ -1,262 +1,265 @@
 /* hapmapPrimateAlleles.c was originally generated by the autoSql program, which also 
  * generated hapmapPrimateAlleles.h and hapmapPrimateAlleles.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 "hapmapPrimateAlleles.h"
 
 
 void hapmapPrimateAllelesStaticLoad(char **row, struct hapmapPrimateAlleles *ret)
 /* Load a row from hapmapPrimateAlleles 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]);
 ret->strand = row[5][0];
 ret->refAllele = row[6][0];
 ret->otherAllele = row[7][0];
 ret->chimpChrom = row[8];
 ret->chimpPos = sqlUnsigned(row[9]);
 ret->chimpStrand = row[10][0];
 ret->chimpAllele = row[11];
 ret->chimpQual = sqlUnsigned(row[12]);
 ret->rhesusChrom = row[13];
 ret->rhesusPos = sqlUnsigned(row[14]);
 ret->rhesusStrand = row[15][0];
 ret->rhesusAllele = row[16];
 ret->rhesusQual = sqlUnsigned(row[17]);
 }
 
 struct hapmapPrimateAlleles *hapmapPrimateAllelesLoad(char **row)
 /* Load a hapmapPrimateAlleles from row fetched with select * from hapmapPrimateAlleles
  * from database.  Dispose of this with hapmapPrimateAllelesFree(). */
 {
 struct hapmapPrimateAlleles *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]);
 ret->strand = row[5][0];
 ret->refAllele = row[6][0];
 ret->otherAllele = row[7][0];
 ret->chimpChrom = cloneString(row[8]);
 ret->chimpPos = sqlUnsigned(row[9]);
 ret->chimpStrand = row[10][0];
 ret->chimpAllele = cloneString(row[11]);
 ret->chimpQual = sqlUnsigned(row[12]);
 ret->rhesusChrom = cloneString(row[13]);
 ret->rhesusPos = sqlUnsigned(row[14]);
 ret->rhesusStrand = row[15][0];
 ret->rhesusAllele = cloneString(row[16]);
 ret->rhesusQual = sqlUnsigned(row[17]);
 return ret;
 }
 
 struct hapmapPrimateAlleles *hapmapPrimateAllelesLoadAll(char *fileName) 
 /* Load all hapmapPrimateAlleles from a whitespace-separated file.
  * Dispose of this with hapmapPrimateAllelesFreeList(). */
 {
 struct hapmapPrimateAlleles *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[18];
 
 while (lineFileRow(lf, row))
     {
     el = hapmapPrimateAllelesLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct hapmapPrimateAlleles *hapmapPrimateAllelesLoadAllByChar(char *fileName, char chopper) 
 /* Load all hapmapPrimateAlleles from a chopper separated file.
  * Dispose of this with hapmapPrimateAllelesFreeList(). */
 {
 struct hapmapPrimateAlleles *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[18];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = hapmapPrimateAllelesLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct hapmapPrimateAlleles *hapmapPrimateAllelesLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all hapmapPrimateAlleles 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 hapmapPrimateAllelesFreeList(). */
 {
 struct hapmapPrimateAlleles *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = hapmapPrimateAllelesLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void hapmapPrimateAllelesSaveToDb(struct sqlConnection *conn, struct hapmapPrimateAlleles *el, char *tableName, int updateSize)
 /* Save hapmapPrimateAlleles 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',%u,%u,'%s',%u,'%c','%c','%c','%s',%u,'%c','%s',%u,'%s',%u,'%c','%s',%u)", 
 	tableName,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->strand,  el->refAllele,  el->otherAllele,  el->chimpChrom,  el->chimpPos,  el->chimpStrand,  el->chimpAllele,  el->chimpQual,  el->rhesusChrom,  el->rhesusPos,  el->rhesusStrand,  el->rhesusAllele,  el->rhesusQual);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
 
 struct hapmapPrimateAlleles *hapmapPrimateAllelesCommaIn(char **pS, struct hapmapPrimateAlleles *ret)
 /* Create a hapmapPrimateAlleles out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new hapmapPrimateAlleles */
 {
 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));
 sqlFixedStringComma(&s, &(ret->refAllele), sizeof(ret->refAllele));
 sqlFixedStringComma(&s, &(ret->otherAllele), sizeof(ret->otherAllele));
 ret->chimpChrom = sqlStringComma(&s);
 ret->chimpPos = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, &(ret->chimpStrand), sizeof(ret->chimpStrand));
 ret->chimpAllele = sqlStringComma(&s);
 ret->chimpQual = sqlUnsignedComma(&s);
 ret->rhesusChrom = sqlStringComma(&s);
 ret->rhesusPos = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, &(ret->rhesusStrand), sizeof(ret->rhesusStrand));
 ret->rhesusAllele = sqlStringComma(&s);
 ret->rhesusQual = sqlUnsignedComma(&s);
 *pS = s;
 return ret;
 }
 
 void hapmapPrimateAllelesFree(struct hapmapPrimateAlleles **pEl)
 /* Free a single dynamically allocated hapmapPrimateAlleles such as created
  * with hapmapPrimateAllelesLoad(). */
 {
 struct hapmapPrimateAlleles *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->chimpChrom);
 freeMem(el->chimpAllele);
 freeMem(el->rhesusChrom);
 freeMem(el->rhesusAllele);
 freez(pEl);
 }
 
 void hapmapPrimateAllelesFreeList(struct hapmapPrimateAlleles **pList)
 /* Free a list of dynamically allocated hapmapPrimateAlleles's */
 {
 struct hapmapPrimateAlleles *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     hapmapPrimateAllelesFree(&el);
     }
 *pList = NULL;
 }
 
 void hapmapPrimateAllelesOutput(struct hapmapPrimateAlleles *el, FILE *f, char sep, char lastSep) 
 /* Print out hapmapPrimateAlleles.  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, "%c", el->strand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%c", el->refAllele);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%c", el->otherAllele);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->chimpChrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->chimpPos);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%c", el->chimpStrand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->chimpAllele);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->chimpQual);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->rhesusChrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->rhesusPos);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%c", el->rhesusStrand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->rhesusAllele);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->rhesusQual);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */