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/protein/kgAliasP/kgAliasP.c src/hg/protein/kgAliasP/kgAliasP.c
index 881e8d2..71c52cc 100644
--- src/hg/protein/kgAliasP/kgAliasP.c
+++ src/hg/protein/kgAliasP/kgAliasP.c
@@ -1,182 +1,182 @@
 /* kgAliasP read and parse the SWISS-PROT data file to generate 
    the protein part of the gene alias list for Known Genes track */
 
 /* 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 "hdb.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "kgAliasP - create gene alias (protein part) .tab files "
   "usage:\n"
   "   kgAliasM xxxx yyyy zzzz\n"
   "            xxxx is genome  database name\n"
   "            yyyy is protein database name\n"
   "            zzzz is .tab output file name\n"
   "Example: kgAliasP hg15 /cluster/store5/fan/data/swissprot/0405/trembl_new.dat new.tab\n");
 }
 
 int main(int argc, char *argv[])
 {
 struct sqlConnection *conn;
     
 FILE *inf;
 FILE *o1;
 
 char cond_str[256];
 char *database;
 char *proteinFileName;
 char *outputFileName;
 char *answer;
 char *alias;
 
 char *id;
 char *chp0, *chp1, *chp2, *chp;
 
 char *kgID;
 char line[2000];
 
 if (argc != 4) usage();
     
 database         = cloneString(argv[1]);
 proteinFileName  = cloneString(argv[2]);
 outputFileName   = cloneString(argv[3]);
 
 conn = hAllocConn(database);
 
 o1 = mustOpen(outputFileName, "w");
     
 if ((inf = mustOpen(proteinFileName, "r")) == NULL)
     {		
     fprintf(stderr, "Can't open file %s.\n", proteinFileName);
     exit(8);
     }
 	
 while (fgets(line, 1000, inf) != NULL)
     {
     chp = strstr(line, "ID   ");
     if (chp != line)
 	{
 	fprintf(stderr, "expected ID line, but got: %s\n", line);
 	exit(1);
 	} 
     chp = chp + strlen("ID   ");
     id = chp;
     chp = strstr(id, " ");
     *chp = '\0';
     id = strdup(id);
         
     sqlSafefFrag(cond_str, sizeof cond_str, "proteinID = '%s'", id);
     answer = sqlGetField(database, "knownGene", "name", cond_str);
     kgID = NULL;
     if (answer != NULL)
 	{
 	kgID = strdup(answer);
 	}
 
     if (fgets(line, 1000, inf) == NULL) 
 	{
 	break;
 	}
     do 
 	{
 	/* "//" signal end of a record */		
 	if ((line[0] == '/') && (line[1] == '/')) break;
 
 	// work on GN (Gene Name) line only
 	chp = strstr(line, "GN   ");
 	if (chp != NULL)
 	    {
 	    chp = line + strlen(line) -2;
 	    if (*chp == '.') 
 		{
 		*chp = '\0';
 		}
 	    else
 		{
 		chp++;
 		*chp = '\0';
 		}
 	    		
 	    chp0 = line + 5;
 	    while (chp0 != NULL)
 	    	{
             	while (*chp0 == ' ') chp0++;
 
             	chp1 = strstr(chp0, " OR ");
             	chp2 = strstr(chp0, " AND ");
 
 		chp = NULL;
 		if (chp1 != NULL)
 		    {
 		    if (chp2 != NULL)
 			{	
 			if (chp1 < chp2)
 			    {
 			    chp = chp1;
 			    }
 			else
 			    {
 			    chp = chp2;
 			    }
 			}
 		    else
 			{
 			chp = chp1;
 			}
 		    }
 
 		if (chp2!= NULL)
 		    {
 		    if (chp1 != NULL)
 			{	
 			if (chp1 < chp2)
 			    {
 			    chp = chp1;
 			    }
 			else
 			    {
 			    chp = chp2;
 			    }
 			}
 		    else
 			{
 			chp = chp2;
 			}
 		    }
 
             	if (chp == NULL)
             	    {
                     alias = strdup(chp0);
                     chp0 = NULL;
                     }
             	else 
                     {
                     *chp = '\0';
                     alias = strdup(chp0);
                     chp0 = chp+4;
                     }
 
  	    	if (kgID != NULL)
 		    {
 		    // clean up "(XXXX" or "XXXX)"
 		    if (*alias == '(') alias++;
 		    chp = strstr(alias, ")");
 		    if (chp != NULL) *chp = '\0';
 
 		    fprintf(o1, "%s\t%s\n", kgID, alias);
 		    }
 	    	}
 	    }
     	} while (fgets(line, 1000, inf) != NULL);
     }
 fclose(o1);
 hFreeConn(&conn);
 return(0);
 }