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/snoRNAs.c src/hg/lib/snoRNAs.c
index 987c527..49b5d2d 100644
--- src/hg/lib/snoRNAs.c
+++ src/hg/lib/snoRNAs.c
@@ -1,235 +1,238 @@
 /* snoRNAs.c was originally generated by the autoSql program, which also 
  * generated snoRNAs.h and snoRNAs.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 "snoRNAs.h"
 
 
 void snoRNAsStaticLoad(char **row, struct snoRNAs *ret)
 /* Load a row from snoRNAs 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->snoScore = sqlFloat(row[6]);
 ret->targetList = row[7];
 ret->orthologs = row[8];
 ret->guideLen = row[9];
 ret->guideStr = row[10];
 ret->guideScore = row[11];
 ret->cBox = row[12];
 ret->dBox = row[13];
 ret->cpBox = row[14];
 ret->dpBox = row[15];
 ret->hmmScore = sqlFloat(row[16]);
 ret->snoscanOutput = row[17];
 }
 
 struct snoRNAs *snoRNAsLoad(char **row)
 /* Load a snoRNAs from row fetched with select * from snoRNAs
  * from database.  Dispose of this with snoRNAsFree(). */
 {
 struct snoRNAs *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->snoScore = sqlFloat(row[6]);
 ret->targetList = cloneString(row[7]);
 ret->orthologs = cloneString(row[8]);
 ret->guideLen = cloneString(row[9]);
 ret->guideStr = cloneString(row[10]);
 ret->guideScore = cloneString(row[11]);
 ret->cBox = cloneString(row[12]);
 ret->dBox = cloneString(row[13]);
 ret->cpBox = cloneString(row[14]);
 ret->dpBox = cloneString(row[15]);
 ret->hmmScore = sqlFloat(row[16]);
 ret->snoscanOutput = cloneString(row[17]);
 return ret;
 }
 
 struct snoRNAs *snoRNAsLoadAll(char *fileName) 
 /* Load all snoRNAs from a whitespace-separated file.
  * Dispose of this with snoRNAsFreeList(). */
 {
 struct snoRNAs *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[18];
 
 while (lineFileRow(lf, row))
     {
     el = snoRNAsLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct snoRNAs *snoRNAsLoadAllByChar(char *fileName, char chopper) 
 /* Load all snoRNAs from a chopper separated file.
  * Dispose of this with snoRNAsFreeList(). */
 {
 struct snoRNAs *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[18];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = snoRNAsLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct snoRNAs *snoRNAsCommaIn(char **pS, struct snoRNAs *ret)
 /* Create a snoRNAs out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new snoRNAs */
 {
 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->snoScore = sqlFloatComma(&s);
 ret->targetList = sqlStringComma(&s);
 ret->orthologs = sqlStringComma(&s);
 ret->guideLen = sqlStringComma(&s);
 ret->guideStr = sqlStringComma(&s);
 ret->guideScore = sqlStringComma(&s);
 ret->cBox = sqlStringComma(&s);
 ret->dBox = sqlStringComma(&s);
 ret->cpBox = sqlStringComma(&s);
 ret->dpBox = sqlStringComma(&s);
 ret->hmmScore = sqlFloatComma(&s);
 ret->snoscanOutput = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void snoRNAsFree(struct snoRNAs **pEl)
 /* Free a single dynamically allocated snoRNAs such as created
  * with snoRNAsLoad(). */
 {
 struct snoRNAs *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->targetList);
 freeMem(el->orthologs);
 freeMem(el->guideLen);
 freeMem(el->guideStr);
 freeMem(el->guideScore);
 freeMem(el->cBox);
 freeMem(el->dBox);
 freeMem(el->cpBox);
 freeMem(el->dpBox);
 freeMem(el->snoscanOutput);
 freez(pEl);
 }
 
 void snoRNAsFreeList(struct snoRNAs **pList)
 /* Free a list of dynamically allocated snoRNAs's */
 {
 struct snoRNAs *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     snoRNAsFree(&el);
     }
 *pList = NULL;
 }
 
 void snoRNAsOutput(struct snoRNAs *el, FILE *f, char sep, char lastSep) 
 /* Print out snoRNAs.  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);
 fprintf(f, "%g", el->snoScore);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->targetList);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->orthologs);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->guideLen);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->guideStr);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->guideScore);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->cBox);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->dBox);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->cpBox);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->dpBox);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%g", el->hmmScore);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->snoscanOutput);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */