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/geneCheck.c src/hg/lib/geneCheck.c
index ca02230..0d16def 100644
--- src/hg/lib/geneCheck.c
+++ src/hg/lib/geneCheck.c
@@ -1,243 +1,246 @@
 /* geneCheck.c was originally generated by the autoSql program, which also 
  * generated geneCheck.h and geneCheck.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 "geneCheck.h"
 
 
 void geneCheckStaticLoad(char **row, struct geneCheck *ret)
 /* Load a row from geneCheck table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->acc = row[0];
 ret->chr = row[1];
 ret->chrStart = sqlUnsigned(row[2]);
 ret->chrEnd = sqlUnsigned(row[3]);
 strcpy(ret->strand, row[4]);
 strcpy(ret->stat, row[5]);
 strcpy(ret->frame, row[6]);
 strcpy(ret->start, row[7]);
 strcpy(ret->stop, row[8]);
 ret->orfStop = sqlUnsigned(row[9]);
 ret->cdsGap = sqlUnsigned(row[10]);
 ret->cdsMult3Gap = sqlUnsigned(row[11]);
 ret->utrGap = sqlUnsigned(row[12]);
 ret->cdsSplice = sqlUnsigned(row[13]);
 ret->utrSplice = sqlUnsigned(row[14]);
 ret->numExons = sqlUnsigned(row[15]);
 ret->numCds = sqlUnsigned(row[16]);
 ret->numUtr5 = sqlUnsigned(row[17]);
 ret->numUtr3 = sqlUnsigned(row[18]);
 ret->numCdsIntrons = sqlUnsigned(row[19]);
 ret->numUtrIntrons = sqlUnsigned(row[20]);
 strcpy(ret->nmd, row[21]);
 ret->causes = row[22];
 }
 
 struct geneCheck *geneCheckLoad(char **row)
 /* Load a geneCheck from row fetched with select * from geneCheck
  * from database.  Dispose of this with geneCheckFree(). */
 {
 struct geneCheck *ret;
 
 AllocVar(ret);
 ret->acc = cloneString(row[0]);
 ret->chr = cloneString(row[1]);
 ret->chrStart = sqlUnsigned(row[2]);
 ret->chrEnd = sqlUnsigned(row[3]);
 strcpy(ret->strand, row[4]);
 strcpy(ret->stat, row[5]);
 strcpy(ret->frame, row[6]);
 strcpy(ret->start, row[7]);
 strcpy(ret->stop, row[8]);
 ret->orfStop = sqlUnsigned(row[9]);
 ret->cdsGap = sqlUnsigned(row[10]);
 ret->cdsMult3Gap = sqlUnsigned(row[11]);
 ret->utrGap = sqlUnsigned(row[12]);
 ret->cdsSplice = sqlUnsigned(row[13]);
 ret->utrSplice = sqlUnsigned(row[14]);
 ret->numExons = sqlUnsigned(row[15]);
 ret->numCds = sqlUnsigned(row[16]);
 ret->numUtr5 = sqlUnsigned(row[17]);
 ret->numUtr3 = sqlUnsigned(row[18]);
 ret->numCdsIntrons = sqlUnsigned(row[19]);
 ret->numUtrIntrons = sqlUnsigned(row[20]);
 strcpy(ret->nmd, row[21]);
 ret->causes = cloneString(row[22]);
 return ret;
 }
 
 struct geneCheck *geneCheckLoadAll(char *fileName) 
 /* Load all geneCheck from a whitespace-separated file.
  * Dispose of this with geneCheckFreeList(). */
 {
 struct geneCheck *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[23];
 
 while (lineFileRow(lf, row))
     {
     el = geneCheckLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct geneCheck *geneCheckLoadAllByChar(char *fileName, char chopper) 
 /* Load all geneCheck from a chopper separated file.
  * Dispose of this with geneCheckFreeList(). */
 {
 struct geneCheck *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[23];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = geneCheckLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct geneCheck *geneCheckCommaIn(char **pS, struct geneCheck *ret)
 /* Create a geneCheck out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new geneCheck */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->acc = sqlStringComma(&s);
 ret->chr = sqlStringComma(&s);
 ret->chrStart = sqlUnsignedComma(&s);
 ret->chrEnd = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 sqlFixedStringComma(&s, ret->stat, sizeof(ret->stat));
 sqlFixedStringComma(&s, ret->frame, sizeof(ret->frame));
 sqlFixedStringComma(&s, ret->start, sizeof(ret->start));
 sqlFixedStringComma(&s, ret->stop, sizeof(ret->stop));
 ret->orfStop = sqlUnsignedComma(&s);
 ret->cdsGap = sqlUnsignedComma(&s);
 ret->cdsMult3Gap = sqlUnsignedComma(&s);
 ret->utrGap = sqlUnsignedComma(&s);
 ret->cdsSplice = sqlUnsignedComma(&s);
 ret->utrSplice = sqlUnsignedComma(&s);
 ret->numExons = sqlUnsignedComma(&s);
 ret->numCds = sqlUnsignedComma(&s);
 ret->numUtr5 = sqlUnsignedComma(&s);
 ret->numUtr3 = sqlUnsignedComma(&s);
 ret->numCdsIntrons = sqlUnsignedComma(&s);
 ret->numUtrIntrons = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, ret->nmd, sizeof(ret->nmd));
 ret->causes = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void geneCheckFree(struct geneCheck **pEl)
 /* Free a single dynamically allocated geneCheck such as created
  * with geneCheckLoad(). */
 {
 struct geneCheck *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->acc);
 freeMem(el->chr);
 freeMem(el->causes);
 freez(pEl);
 }
 
 void geneCheckFreeList(struct geneCheck **pList)
 /* Free a list of dynamically allocated geneCheck's */
 {
 struct geneCheck *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     geneCheckFree(&el);
     }
 *pList = NULL;
 }
 
 void geneCheckOutput(struct geneCheck *el, FILE *f, char sep, char lastSep) 
 /* Print out geneCheck.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->acc);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->chr);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->chrStart);
 fputc(sep,f);
 fprintf(f, "%u", el->chrEnd);
 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->stat);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->frame);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->start);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->stop);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->orfStop);
 fputc(sep,f);
 fprintf(f, "%u", el->cdsGap);
 fputc(sep,f);
 fprintf(f, "%u", el->cdsMult3Gap);
 fputc(sep,f);
 fprintf(f, "%u", el->utrGap);
 fputc(sep,f);
 fprintf(f, "%u", el->cdsSplice);
 fputc(sep,f);
 fprintf(f, "%u", el->utrSplice);
 fputc(sep,f);
 fprintf(f, "%u", el->numExons);
 fputc(sep,f);
 fprintf(f, "%u", el->numCds);
 fputc(sep,f);
 fprintf(f, "%u", el->numUtr5);
 fputc(sep,f);
 fprintf(f, "%u", el->numUtr3);
 fputc(sep,f);
 fprintf(f, "%u", el->numCdsIntrons);
 fputc(sep,f);
 fprintf(f, "%u", el->numUtrIntrons);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->nmd);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->causes);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */