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/makeDb/outside/hgSoftberryHom/hgSoftberryHom.c src/hg/makeDb/outside/hgSoftberryHom/hgSoftberryHom.c
index 12626d6..22bed92 100644
--- src/hg/makeDb/outside/hgSoftberryHom/hgSoftberryHom.c
+++ src/hg/makeDb/outside/hgSoftberryHom/hgSoftberryHom.c
@@ -1,107 +1,107 @@
 /* hgSoftberryHom - Make table storing Softberry protein homology information. */
 
 /* Copyright (C) 2013 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 "hash.h"
 #include "dystring.h"
 #include "jksql.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "hgSoftberryHom - Make table storing Softberry protein homology information\n"
   "usage:\n"
   "   hgSoftberryHom database file(s).pro\n");
 }
 
 void makeTabLines(char *fileName, FILE *f)
 /* Loop through file and write out tab-separated records to f. */
 {
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *line, *s, *e, *protParts[128];
 int lineSize, protCount;
 int i;
 char *label, *gi;
 
 while (lineFileNext(lf, &line, &lineSize))
     {
     if (line[0] != '>')
         continue;
     line += 1;
     label = nextWord(&line);
     if (label == NULL)
 	errAbort("Bad format A line %d of %s\n", lf->lineIx, lf->fileName);
     if ((s = strstr(line, "##")) == NULL)
         continue;
     s += 2;
     if ((e = strstr(line, "##")) != NULL)
         *e = 0;
     s = trimSpaces(s);
     protCount = chopString(s, "\001", protParts, ArraySize(protParts));
     if (protCount < 1)
 	errAbort("Bad format C line %d of %s\n", lf->lineIx, lf->fileName);
     for (i=0; i<protCount; ++i)
         {
 	s = protParts[i];
 	gi = nextWord(&s);
 	if (s == NULL) s = "";
 	fprintf(f, "%s\t%s\t%s\n", label, gi, s);
 	}
     }
 lineFileClose(&lf);
 }
 
 /* #Protein homologies behind Softberry genes */
 char *createTable = NOSQLINJ "CREATE TABLE softberryHom (\n"
     "name varchar(255) not null,	# Softberry gene name\n"
     "giString varchar(255) not null,	# String with Genbank gi and accession\n"
     "description longblob not null,	# Freeform (except for no tabs) description\n"
               "#Indices\n"
     "PRIMARY KEY(name)\n"
 ")\n";
 
 void hgSoftberryHom(char *database, int fileCount, char *files[])
 /* hgSoftberryHom - Make table storing Softberry protein homology information. */
 {
 int i;
 char *fileName;
 char *table = "softberryHom";
 char *tabFileName = "softberryHom.tab";
 FILE *f = mustOpen(tabFileName, "w");
 struct sqlConnection *conn = NULL;
 struct dyString *ds = newDyString(2048);
 
 for (i=0; i<fileCount; ++i)
     {
     fileName = files[i];
     printf("Processing %s\n", fileName);
     makeTabLines(fileName, f);
     }
 carefulClose(&f);
 
 /* Create table if it doesn't exist, delete whatever is
  * already in it, and fill it up from tab file. */
 conn = sqlConnect(database);
 printf("Loading %s table\n", table);
 sqlMaybeMakeTable(conn, table, createTable);
 sqlDyStringPrintf(ds, "DELETE from %s", table);
 sqlUpdate(conn, ds->string);
 dyStringClear(ds);
 sqlDyStringPrintf(ds, "LOAD data local infile '%s' into table %s", 
     tabFileName, table);
 sqlUpdate(conn, ds->string);
 sqlDisconnect(&conn);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 if (argc < 3)
     usage();
 hgSoftberryHom(argv[1], argc-2, argv+2);
 return 0;
 }