4898794edd81be5285ea6e544acbedeaeb31bf78
max
  Tue Nov 23 08:10:57 2021 -0800
Fixing pointers to README file for license in all source code files. refs #27614

diff --git src/hg/lib/cgapSage/cgapSageLib.c src/hg/lib/cgapSage/cgapSageLib.c
index 31f4ea0..167c26b 100644
--- src/hg/lib/cgapSage/cgapSageLib.c
+++ src/hg/lib/cgapSage/cgapSageLib.c
@@ -1,311 +1,311 @@
 /* cgapSageLib.c was originally generated by the autoSql program, which also 
  * generated cgapSageLib.h and cgapSageLib.sql.  This module links the database and
  * the RAM representation of objects. */
 
 /* Copyright (C) 2011 The Regents of the University of California 
- * See README in this or parent directory for licensing information. */
+ * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "cgapSage/cgapSageLib.h"
 
 
 /* definitions for sex column */
 static char *values_sex[] = {"male", "female", NULL};
 static struct hash *valhash_sex = NULL;
 
 void cgapSageLibStaticLoad(char **row, struct cgapSageLib *ret)
 /* Load a row from cgapSageLib table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->libId = sqlUnsigned(row[0]);
 ret->oldLibName = row[1];
 ret->newLibName = row[2];
 ret->totalTags = sqlUnsigned(row[3]);
 ret->totalTagsNoLinker = sqlUnsigned(row[4]);
 ret->uniqueTags = sqlUnsigned(row[5]);
 ret->quality = sqlUnsigned(row[6]);
 ret->tissue = row[7];
 ret->tissuePrep = row[8];
 ret->cellType = row[9];
 ret->keywords = row[10];
 ret->age = row[11];
 ret->sex = sqlSetParse(row[12], values_sex, &valhash_sex);
 ret->mutations = row[13];
 ret->otherInfo = row[14];
 ret->tagEnzyme = row[15];
 ret->anchorEnzyme = row[16];
 ret->cellSupplier = row[17];
 ret->libProducer = row[18];
 ret->laboratory = row[19];
 ret->refs = row[20];
 }
 
 struct cgapSageLib *cgapSageLibLoad(char **row)
 /* Load a cgapSageLib from row fetched with select * from cgapSageLib
  * from database.  Dispose of this with cgapSageLibFree(). */
 {
 struct cgapSageLib *ret;
 
 AllocVar(ret);
 ret->libId = sqlUnsigned(row[0]);
 ret->oldLibName = cloneString(row[1]);
 ret->newLibName = cloneString(row[2]);
 ret->totalTags = sqlUnsigned(row[3]);
 ret->totalTagsNoLinker = sqlUnsigned(row[4]);
 ret->uniqueTags = sqlUnsigned(row[5]);
 ret->quality = sqlUnsigned(row[6]);
 ret->tissue = cloneString(row[7]);
 ret->tissuePrep = cloneString(row[8]);
 ret->cellType = cloneString(row[9]);
 ret->keywords = cloneString(row[10]);
 ret->age = cloneString(row[11]);
 ret->sex = sqlSetParse(row[12], values_sex, &valhash_sex);
 ret->mutations = cloneString(row[13]);
 ret->otherInfo = cloneString(row[14]);
 ret->tagEnzyme = cloneString(row[15]);
 ret->anchorEnzyme = cloneString(row[16]);
 ret->cellSupplier = cloneString(row[17]);
 ret->libProducer = cloneString(row[18]);
 ret->laboratory = cloneString(row[19]);
 ret->refs = cloneString(row[20]);
 return ret;
 }
 
 struct cgapSageLib *cgapSageLibLoadAll(char *fileName) 
 /* Load all cgapSageLib from a whitespace-separated file.
  * Dispose of this with cgapSageLibFreeList(). */
 {
 struct cgapSageLib *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[21];
 
 while (lineFileRow(lf, row))
     {
     el = cgapSageLibLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct cgapSageLib *cgapSageLibLoadAllByChar(char *fileName, char chopper) 
 /* Load all cgapSageLib from a chopper separated file.
  * Dispose of this with cgapSageLibFreeList(). */
 {
 struct cgapSageLib *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[21];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = cgapSageLibLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct cgapSageLib *cgapSageLibLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all cgapSageLib 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 cgapSageLibFreeList(). */
 {
 struct cgapSageLib *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = cgapSageLibLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 struct cgapSageLib *cgapSageLibCommaIn(char **pS, struct cgapSageLib *ret)
 /* Create a cgapSageLib out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new cgapSageLib */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->libId = sqlUnsignedComma(&s);
 ret->oldLibName = sqlStringComma(&s);
 ret->newLibName = sqlStringComma(&s);
 ret->totalTags = sqlUnsignedComma(&s);
 ret->totalTagsNoLinker = sqlUnsignedComma(&s);
 ret->uniqueTags = sqlUnsignedComma(&s);
 ret->quality = sqlUnsignedComma(&s);
 ret->tissue = sqlStringComma(&s);
 ret->tissuePrep = sqlStringComma(&s);
 ret->cellType = sqlStringComma(&s);
 ret->keywords = sqlStringComma(&s);
 ret->age = sqlStringComma(&s);
 ret->sex = sqlSetComma(&s, values_sex, &valhash_sex);
 ret->mutations = sqlStringComma(&s);
 ret->otherInfo = sqlStringComma(&s);
 ret->tagEnzyme = sqlStringComma(&s);
 ret->anchorEnzyme = sqlStringComma(&s);
 ret->cellSupplier = sqlStringComma(&s);
 ret->libProducer = sqlStringComma(&s);
 ret->laboratory = sqlStringComma(&s);
 ret->refs = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void cgapSageLibFree(struct cgapSageLib **pEl)
 /* Free a single dynamically allocated cgapSageLib such as created
  * with cgapSageLibLoad(). */
 {
 struct cgapSageLib *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->oldLibName);
 freeMem(el->newLibName);
 freeMem(el->tissue);
 freeMem(el->tissuePrep);
 freeMem(el->cellType);
 freeMem(el->keywords);
 freeMem(el->age);
 freeMem(el->mutations);
 freeMem(el->otherInfo);
 freeMem(el->tagEnzyme);
 freeMem(el->anchorEnzyme);
 freeMem(el->cellSupplier);
 freeMem(el->libProducer);
 freeMem(el->laboratory);
 freeMem(el->refs);
 freez(pEl);
 }
 
 void cgapSageLibFreeList(struct cgapSageLib **pList)
 /* Free a list of dynamically allocated cgapSageLib's */
 {
 struct cgapSageLib *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     cgapSageLibFree(&el);
     }
 *pList = NULL;
 }
 
 void cgapSageLibOutput(struct cgapSageLib *el, FILE *f, char sep, char lastSep) 
 /* Print out cgapSageLib.  Separate fields with sep. Follow last field with lastSep. */
 {
 fprintf(f, "%u", el->libId);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->oldLibName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->newLibName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->totalTags);
 fputc(sep,f);
 fprintf(f, "%u", el->totalTagsNoLinker);
 fputc(sep,f);
 fprintf(f, "%u", el->uniqueTags);
 fputc(sep,f);
 fprintf(f, "%u", el->quality);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->tissue);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->tissuePrep);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->cellType);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->keywords);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->age);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 sqlSetPrint(f, el->sex, values_sex);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->mutations);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->otherInfo);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->tagEnzyme);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->anchorEnzyme);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->cellSupplier);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->libProducer);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->laboratory);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->refs);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 struct hash *getTotTagsHash(struct cgapSageLib *libs)
 /* Read in the library file and hash up the total tags. */
 {
 struct hash *totTagsHash = newHash(9);
 struct cgapSageLib *lib;
 for (lib = libs; lib != NULL; lib = lib->next)
     {
     char buf[16];
     safef(buf, sizeof(buf), "%d", lib->libId);
     hashAddInt(totTagsHash, buf, (int)lib->totalTags);
     }
 return totTagsHash;
 }
 
 struct hash *getTotTagsHashFromFile(char *libFile)
 /* Load a file then call getTotTagsHash. */
 {
 struct cgapSageLib *libs = cgapSageLibLoadAll(libFile);
 struct hash *libTotHash = getTotTagsHash(libs);
 cgapSageLibFreeList(&libs);
 return libTotHash;
 }