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/hgNetDist/hprdP2p.c src/hg/near/hgNetDist/hprdP2p.c
index 9db25c0..4578175 100644
--- src/hg/near/hgNetDist/hprdP2p.c
+++ src/hg/near/hgNetDist/hprdP2p.c
@@ -1,115 +1,115 @@
 /* Copyright (C) 2007 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. */
 
 /* hprdP2p - Create hprd.p2p tab file by reading HPRD FLAT_FILES.
  *   It is assumed that the HPRD flat files have been decompressed in
  *   a directory like /cluster/data/hg18/p2p/hprd/FLAT_FILES/ 
  *   The data has this structure:
 
 [hgwdev:FLAT_FILES> head BINARY_PROTEIN_PROTEIN_INTERACTIONS.txt
 SMAD4   02995   NP_005350.1     SMAD9   04484   BAA21128.1      yeast 2-hybrid  16189514,15231748
 
 col 2 col 5 dist 1.0
 
 [hgwdev:FLAT_FILES> head PROTEIN_COMPLEXES.txt
 COM_1   00011   ASCL1   NP_004307.2     in vivo 8900141,8948587
 COM_1   00918   TCF3    NP_003191.1     in vivo 8900141,8948587
 COM_1   02809   MEF2C   NP_002388.2     in vivo 8900141,8948587
 
 All pairs from col 2 for same col 1 with dist 1.5
 
  */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "dystring.h"
 #include "options.h"
 #include "jksql.h"
 #include "hdb.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "hprdP2p - Create hprd.p2p tab file using HPRD flat file for input to hgNetDist\n"
   "usage:\n"
   "   hprdP2p hprdBinaryPPI hprdComplexes hprd.p2p\n"
   );
 
   /*
   "options:\n"
   "   -xxx=XXX\n"
 
         hprdP2p -verbose=2 \
                 /cluster/data/hg18/p2p/hprd/FLAT_FILES/BINARY_PROTEIN_PROTEIN_INTERACTIONS.txt \
                 /cluster/data/hg18/p2p/hprd/FLAT_FILES/PROTEIN_COMPLEXES.txt \
                 hprd.p2p
   */
 }
 
 static struct optionSpec options[] = {
    {NULL, 0},
 };
 
 void iterateComplex(char *ids[100], int max, FILE *f, char *complexId)
 /* Iterate through all pairs, assign dist 1.5 
  * to indicate not necessarily a direct interaction
  * between pairs in the complex */
 {
 int i=0,j=0;
 if (max==1)
     verbose(2,"weird complex:%s has max==1, only 1 member\n",complexId);
 for(i=0;i<max;++i)
     for(j=i+1;j<max;++j)
 	fprintf(f,"%s\t%s\t1.5\n",ids[i],ids[j]);
 }
 
 void hprdP2p(char *hprdBinaryPPI, char *hprdComplexes, char *outTab)
 /* hprdP2p - Create hprd.p2p tab file from HPRD flat files for use with hgNetDist. */
 {
 FILE *f = mustOpen(outTab, "w");
 char *row[8];
 char *row2[6];
 char *ids[100];
 struct lineFile *lf = lineFileOpen(hprdBinaryPPI, TRUE);
 while (lineFileRowTab(lf, row))
     {
     char *hprdId1 = row[1];
     char *hprdId2 = row[4];
     fprintf(f,"%s\t%s\t1.0\n",hprdId1,hprdId2);
     }
 lineFileClose(&lf);
 
 lf = lineFileOpen(hprdComplexes, TRUE);
 char *lastComplex = "";
 int i = 0;
 while (lineFileRowTab(lf, row2))
     {
     char *complexId = row2[0];
     char *hprdId = row2[1];
     if (sameString(hprdId,"None"))
 	continue;
     if (!sameString(complexId,lastComplex))
 	{
     	iterateComplex(ids, i, f, lastComplex);
 	i = 0;
 	lastComplex = complexId;
 	}
     ids[i++] = cloneString(hprdId);
     }
 iterateComplex(ids, i, f, lastComplex);
 lineFileClose(&lf);
 
 carefulClose(&f);
 
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 4)
     usage();
 hprdP2p(argv[1],argv[2],argv[3]);
 return 0;
 }