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/gisaid/gisaidSample/sequence.c src/hg/gisaid/gisaidSample/sequence.c
index 461108e..d4bcba2 100644
--- src/hg/gisaid/gisaidSample/sequence.c
+++ src/hg/gisaid/gisaidSample/sequence.c
@@ -1,127 +1,127 @@
 /* sequence - do Sequence section. */
 
 /* 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 "hash.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "cheapcgi.h"
 #include "spDb.h"
 #include "gisaidSample.h"
 #include "hdb.h"
 #include "net.h"
 #include "hPrint.h"
 
 
 static boolean sequenceExists(struct section *section, 
 	struct sqlConnection *conn, char *sampleId)
 /* Return TRUE if sequenceAll table exists and it has an entry with the gene symbol */
 {
 if (sqlTableExists(conn, "dnaSeq") == TRUE)
     {
     return(TRUE);
     }
 return(FALSE);
 }
 
 static void sequencePrint(struct section *section, 
 	struct sqlConnection *conn, char *sampleId)
 /* Print out Sequence section. */
 {
 char query[256];
 struct sqlResult *sr;
 char **row;
 char *seq, *seqId;
 
 int i, l;
 char *chp;
 char *subjId, *gene;
 
 printf("<B>DNA Sequences</B><BR>");
 sqlSafef(query, sizeof(query), 
       "select seqId, seq, strain, geneSymbol from h1n1SeqXref, dnaSeq where islId = '%s' and id = seqId order by seqId", sampleId);
 sr = sqlMustGetResult(conn, query);
 row = sqlNextRow(sr);
 if (row == NULL) printf("<BR>Not available.<BR><BR>");
 
 while (row != NULL) 
     {
     seqId    = row[0];
     seq	     = row[1];
     subjId   = row[2];
     gene     = row[3];
 
     l =strlen(seq);
     hPrintf("<A NAME=\"%s\">\n", seqId);
     hPrintf("<pre>\n");
     hPrintf("%c%s", '>', seqId);
     hPrintf("%s%s", " | ", sampleId);
     hPrintf("%s%s", " | ", subjId);
     hPrintf("%s%s", " | ", gene);
     chp = seq;
     for (i=0; i<l; i++)
 	{
 	if ((i%50) == 0) hPrintf("\n");
 	hPrintf("%c", *chp);
 	chp++;
 	}
     hPrintf("</pre>");
     fflush(stdout);
     
     row = sqlNextRow(sr);
     }
 sqlFreeResult(&sr);
 
 printf("<B>Protein Sequences</B><BR>");
 sqlSafef(query, sizeof(query), 
       "select aaSeqId, seq, strain from h1n1SeqXref i, gisaidXref, aaSeq where islId = '%s' and i.seqId=dnaSeqId and aaSeqId = id order by aaSeqId", sampleId);
 sr = sqlMustGetResult(conn, query);
 row = sqlNextRow(sr);
 if (row == NULL) printf("<BR>Not available.<BR>");
     
 while (row != NULL) 
     {
     seqId    = row[0];
     seq	     = row[1];
     subjId   = row[2];
 
     l =strlen(seq);
     hPrintf("<A NAME=\"%s\">\n", seqId);
 
     hPrintf("<pre>\n");
     hPrintf("%c%s", '>', seqId);
     hPrintf("%s%s", " | ", sampleId);
     hPrintf("%s%s", " | ", subjId);
     //hPrintf("<A NAME=\"%s\">\n", seqId);
     //hPrintf("><A HREF=\"../cgi-bin/pbGsid?proteinID=%s\"", seqId);
     //hPrintf("%c%s", '>', seqId);
     //hPrintf("</A>");
     //hPrintf("%c%s", ':', sampleId);
     chp = seq;
     for (i=0; i<l; i++)
 	{
 	if ((i%50) == 0) hPrintf("\n");
 	hPrintf("%c", *chp);
 	chp++;
 	}
     hPrintf("</pre>");
     fflush(stdout);
     
     row = sqlNextRow(sr);
     }
 sqlFreeResult(&sr);
 return;
 }
 
 struct section *sequenceSection(struct sqlConnection *conn, 
 	struct hash *sectionRa)
 /* Create sequence section. */
 {
 struct section *section = sectionNew(sectionRa, "sequence");
 section->exists = sequenceExists;
 section->print = sequencePrint;
 return section;
 }