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/oneShot/doEvoFold/doEvoFold.c src/hg/oneShot/doEvoFold/doEvoFold.c
index 4f82a33..dc04b69 100644
--- src/hg/oneShot/doEvoFold/doEvoFold.c
+++ src/hg/oneShot/doEvoFold/doEvoFold.c
@@ -1,84 +1,84 @@
 /* doEvoFold - This is a one shot program used for the EvoFold track build */
 
 /* 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 "hCommon.h"
 #include "dnautil.h"
 #include "hdb.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "doEvoFold - This program builds Java command lines needed to generate .png files of EvoFold RNA structures.\n"
   "usage:\n"
   "   doEvoFold db outFileName chrom\n"
   "      db is the database name\n"
   "      outFileName is the filename of the output file, which consists of Java command lines\n"
   "      chrom is the target chromosome name\n"
   "example: doEvoFold hg19 dochr22 chr22\n");
 }
 
 char *avId, *omimId;
 FILE *outf;
 char *tgtChrom;
 
 char *secStr, *id, *chrom;
 int  chromStart, chromEnd;
 char strand;
 char javaCmd[4096];
 
 int main(int argc, char *argv[])
 {
 char *database;
 char *outFn;
 struct dnaSeq *seq;
 
 struct sqlConnection *conn2;
 char query2[256];
 struct sqlResult *sr2;
 char **row2;
 
 if (argc != 4) usage();
 
 database = argv[1];
 conn2= hAllocConn(database);
 
 outFn   = argv[2];
 outf    = mustOpen(outFn, "w");
 
 tgtChrom = argv[3];
 
 sqlSafef(query2, sizeof query2, "select secStr, name, chrom, chromStart, chromEnd, strand from evofold where chrom='%s'", tgtChrom);
 sr2 = sqlMustGetResult(conn2, query2);
 row2 = sqlNextRow(sr2);
 while (row2 != NULL)
     {
     secStr   	= row2[0];
     id  	= row2[1];
     chrom 	= row2[2];
     chromStart 	= atoi(row2[3]);
     chromEnd   	= atoi(row2[4]);
     strand     	= *row2[5];
     seq = hChromSeq(database, chrom, chromStart, chromEnd);
     touppers(seq->dna);
     if (strand == '-')
         reverseComplement(seq->dna, seq->size);
 
     memSwapChar(seq->dna, seq->size, 'T', 'U');
 
     safef(javaCmd, sizeof(javaCmd),
        "java -cp VARNAv3-7.jar fr.orsay.lri.varna.applications.VARNAcmd -sequenceDBN %s -structureDBN '%s' -o evoFold/%s/%s.png",
           seq->dna,  secStr, chrom, id);
     
     fprintf(outf, "%s\n", javaCmd);
 
     row2 = sqlNextRow(sr2);
     }
 sqlFreeResult(&sr2);
 
 fclose(outf);
 hFreeConn(&conn2);
 return(0);
 }