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/dbRIP.c src/hg/lib/dbRIP.c
index 8ce2fe6..034f943 100644
--- src/hg/lib/dbRIP.c
+++ src/hg/lib/dbRIP.c
@@ -1,301 +1,304 @@
 /* dbRIP.c was originally generated by the autoSql program, which also 
  * generated dbRIP.h and dbRIP.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 "dbRIP.h"
 
 
 void dbRIPStaticLoad(char **row, struct dbRIP *ret)
 /* Load a row from dbRIP 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]);
 ret->originalId = row[6];
 ret->forwardPrimer = row[7];
 ret->reversePrimer = row[8];
 ret->polyClass = row[9];
 ret->polyFamily = row[10];
 ret->polySubfamily = row[11];
 ret->polySeq = row[12];
 ret->polySource = row[13];
 ret->reference = row[14];
 ret->ascertainingMethod = row[15];
 ret->remarks = row[16];
 ret->tm = atof(row[17]);
 ret->filledSize = sqlSigned(row[18]);
 ret->emptySize = sqlSigned(row[19]);
 ret->disease = row[20];
 ret->genoRegion = row[21];
 }
 
 struct dbRIP *dbRIPLoad(char **row)
 /* Load a dbRIP from row fetched with select * from dbRIP
  * from database.  Dispose of this with dbRIPFree(). */
 {
 struct dbRIP *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]);
 ret->originalId = cloneString(row[6]);
 ret->forwardPrimer = cloneString(row[7]);
 ret->reversePrimer = cloneString(row[8]);
 ret->polyClass = cloneString(row[9]);
 ret->polyFamily = cloneString(row[10]);
 ret->polySubfamily = cloneString(row[11]);
 ret->polySeq = cloneString(row[12]);
 ret->polySource = cloneString(row[13]);
 ret->reference = cloneString(row[14]);
 ret->ascertainingMethod = cloneString(row[15]);
 ret->remarks = cloneString(row[16]);
 ret->tm = atof(row[17]);
 ret->filledSize = sqlSigned(row[18]);
 ret->emptySize = sqlSigned(row[19]);
 ret->disease = cloneString(row[20]);
 ret->genoRegion = cloneString(row[21]);
 return ret;
 }
 
 struct dbRIP *dbRIPLoadAll(char *fileName) 
 /* Load all dbRIP from a whitespace-separated file.
  * Dispose of this with dbRIPFreeList(). */
 {
 struct dbRIP *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[22];
 
 while (lineFileRow(lf, row))
     {
     el = dbRIPLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct dbRIP *dbRIPLoadAllByChar(char *fileName, char chopper) 
 /* Load all dbRIP from a chopper separated file.
  * Dispose of this with dbRIPFreeList(). */
 {
 struct dbRIP *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[22];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = dbRIPLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct dbRIP *dbRIPLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all dbRIP 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 dbRIPFreeList(). */
 {
 struct dbRIP *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = dbRIPLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void dbRIPSaveToDb(struct sqlConnection *conn, struct dbRIP *el, char *tableName, int updateSize)
 /* Save dbRIP 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,'%s','%s','%s','%s','%s','%s','%s',%s,'%s',%s,'%s','%s',%g,%d,%d,'%s','%s')", 
 	tableName,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->strand,  el->originalId,  el->forwardPrimer,  el->reversePrimer,  el->polyClass,  el->polyFamily,  el->polySubfamily,  el->polySeq,  el->polySource,  el->reference,  el->ascertainingMethod,  el->remarks,  el->tm,  el->filledSize,  el->emptySize,  el->disease,  el->genoRegion);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
 
 struct dbRIP *dbRIPCommaIn(char **pS, struct dbRIP *ret)
 /* Create a dbRIP out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new dbRIP */
 {
 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));
 ret->originalId = sqlStringComma(&s);
 ret->forwardPrimer = sqlStringComma(&s);
 ret->reversePrimer = sqlStringComma(&s);
 ret->polyClass = sqlStringComma(&s);
 ret->polyFamily = sqlStringComma(&s);
 ret->polySubfamily = sqlStringComma(&s);
 ret->polySeq = sqlStringComma(&s);
 ret->polySource = sqlStringComma(&s);
 ret->reference = sqlStringComma(&s);
 ret->ascertainingMethod = sqlStringComma(&s);
 ret->remarks = sqlStringComma(&s);
 ret->tm = sqlFloatComma(&s);
 ret->filledSize = sqlSignedComma(&s);
 ret->emptySize = sqlSignedComma(&s);
 ret->disease = sqlStringComma(&s);
 ret->genoRegion = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void dbRIPFree(struct dbRIP **pEl)
 /* Free a single dynamically allocated dbRIP such as created
  * with dbRIPLoad(). */
 {
 struct dbRIP *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->originalId);
 freeMem(el->forwardPrimer);
 freeMem(el->reversePrimer);
 freeMem(el->polyClass);
 freeMem(el->polyFamily);
 freeMem(el->polySubfamily);
 freeMem(el->polySeq);
 freeMem(el->polySource);
 freeMem(el->reference);
 freeMem(el->ascertainingMethod);
 freeMem(el->remarks);
 freeMem(el->disease);
 freeMem(el->genoRegion);
 freez(pEl);
 }
 
 void dbRIPFreeList(struct dbRIP **pList)
 /* Free a list of dynamically allocated dbRIP's */
 {
 struct dbRIP *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     dbRIPFree(&el);
     }
 *pList = NULL;
 }
 
 void dbRIPOutput(struct dbRIP *el, FILE *f, char sep, char lastSep) 
 /* Print out dbRIP.  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(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->originalId);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->forwardPrimer);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->reversePrimer);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->polyClass);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->polyFamily);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->polySubfamily);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->polySeq);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->polySource);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->reference);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->ascertainingMethod);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->remarks);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%g", el->tm);
 fputc(sep,f);
 fprintf(f, "%d", el->filledSize);
 fputc(sep,f);
 fprintf(f, "%d", el->emptySize);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->disease);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->genoRegion);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */