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/near/hgNear/afiAli.c src/hg/near/hgNear/afiAli.c
index 180ebba..ded0411 100644
--- src/hg/near/hgNear/afiAli.c
+++ src/hg/near/hgNear/afiAli.c
@@ -1,88 +1,88 @@
 /* afiAli.c - show affine alignment. */
 
 /* 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 "obscure.h"
 #include "dnaseq.h"
 #include "fa.h"
 #include "axt.h"
 #include "hgNear.h"
 
 
 static bioSeq *getSeq(struct sqlConnection *conn, char *geneId, 
 	struct column *nameCol, char *tableId)
 /* Get sequence from table. */
 {
 struct genePos *gp = knownPosOne(conn, geneId);
 
 if (gp == NULL)
     {
     warn("Can't find %s in database", geneId);
     return NULL;
     }
 else
     {
     char *table = genomeSetting(tableId);
     char query[512];
     struct sqlResult *sr;
     char **row;
     bioSeq *seq = NULL;
     char *name;
     if (nameCol != NULL)
 	name = nameCol->cellVal(nameCol, gp, conn);
     else
         name = cloneString(geneId);
     sqlSafef(query, sizeof(query), 
 	"select seq from %s where name = '%s'", table, geneId);
     sr = sqlGetResult(conn, query);
     if ((row = sqlNextRow(sr)) != NULL)
 	{
 	AllocVar(seq);
 	seq->name = name;
 	seq->dna = cloneString(row[0]);
 	seq->size = strlen(seq->dna);
 	}
     sqlFreeResult(&sr);
     return seq;
     }
 }
 
 void doAffineAlignment(struct sqlConnection *conn)
 /* Put up page that shows affine alignment. */
 {
 struct column *nameCol = findNamedColumn("name");
 char *aId = cartString(cart, affineAliVarName);
 char *bId = cartString(cart, searchVarName);
 bioSeq *a = getSeq(conn, aId, nameCol, "pepTable");
 bioSeq *b = getSeq(conn, bId, nameCol, "pepTable");
 struct axtScoreScheme *ss = axtScoreSchemeProteinDefault();
 makeTitle("Affine Alignment", NULL);
 
 if (a != NULL && b != NULL)
     {
     printf("<TT><PRE>");
     if (axtAffineSmallEnough(a->size, b->size))
 	{
 	struct axt *axt = axtAffine(a, b, ss);
 	if (axt != NULL)
 	    {
 	    printf("Alignment between %s (top %s %daa) and %s (bottom %s %daa) score %d\n\n",
 		    a->name, aId, a->size, b->name, bId, b->size, axt->score);
 	    axtPrintTraditional(axt, 60, ss, stdout);
 	    axtFree(&axt);
 	    }
 	else
 	    {
 	    printf("%s and %s don't align\n", a->name, b->name);
 	    }
 	}
     else
 	{
 	printf("Sorry, %s (%d amino acids) and %s (%d amino acids) are too big to align",
 	    a->name, a->size, b->name, b->size);
 	}
     printf("</PRE></TT>");
     }
 }