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/txGraph/txgToXml/txgToXml.c src/hg/txGraph/txgToXml/txgToXml.c
index 685c9b6..b2a4045 100644
--- src/hg/txGraph/txgToXml/txgToXml.c
+++ src/hg/txGraph/txgToXml/txgToXml.c
@@ -1,106 +1,106 @@
 /* txgToXml - Convert txg to an XML format.. */
 
 /* 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. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "geneGraph.h"
 #include "txGraph.h"
 
 boolean showEvidence = TRUE;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "txgToXml - Convert txg to an XML format.\n"
   "usage:\n"
   "   txgToXml in.txg out.xml\n"
   "options:\n"
   "   -noEvidence\n"
   );
 }
 
 static struct optionSpec options[] = {
    {"noEvidence", OPTION_BOOLEAN},
    {NULL, 0},
 };
 
 void txgWriteXml(struct txGraph *graph, FILE *f)
 /* Write out graph as xml. */
 {
 fprintf(f, "  <txGraph name=\"%s\" tName=\"%s\" strand=\"%s\" tStart=\"%d\" tEnd=\"%d\" vertexCount=\"%d\" edgeCount=\"%d\" sourceCount=\"%d\">\n",
 	graph->name, graph->tName, graph->strand, graph->tStart, graph->tEnd, graph->vertexCount, graph->edgeCount,
 	graph->sourceCount);
 int i;
 for (i=0; i<graph->vertexCount; ++i)
     {
     struct txVertex *v = &graph->vertices[i];
     fprintf(f, "    <vertex type=\"%s\" pos=\"%d\" i=\"%d\"/>\n",
     	ggVertexTypeAsString(v->type), v->position, i);
     }
 struct txEdge *edge;
 for (edge = graph->edgeList; edge != NULL; edge = edge->next)
     {
     int i1 = edge->startIx;
     int i2 = edge->endIx;
     char *t1 = ggVertexTypeAsString(graph->vertices[i1].type);
     char *t2 = ggVertexTypeAsString(graph->vertices[i2].type);
     int x1 = graph->vertices[i1].position;
     int x2 = graph->vertices[i2].position;
     fprintf(f, "    <edge type=\"%s\" t1=\"%s\" t2=\"%s\" size=\"%d\" x1=\"%d\" x2=\"%d\" i1=\"%d\" i2=\"%d\"", 
         (edge->type == ggExon ? "exon  " : "intron"),
 	t1, t2, x2-x1, x1, x2, i1, i2);
     if (showEvidence)
         {
 	fprintf(f, ">\n");
 	struct txEvidence *ev;	
 	for (ev = edge->evList; ev != NULL; ev = ev->next)
 	    {
 	    struct txSource *source = &graph->sources[ev->sourceId];
 	    fprintf(f, "      <ev acc=\"%s\" x1=\"%d\" x2=\"%d\"/>\n",
 	    	source->accession, ev->start, ev->end);
 	    }
 	fprintf(f, "    </edge>\n");
 	}
     else
         {
 	fprintf(f, "/>\n");
 	}
     }
 for (i=0; i<graph->sourceCount; ++i)
     {
     struct txSource *source = &graph->sources[i];
     fprintf(f, "    <source type=\"%s\" acc=\"%s\"/>\n", 
     	source->type, source->accession);
     }
 fprintf(f, "  </txGraph>\n");
 }
 
 void txgToXml(char *inTxg, char *outXml)
 /* txgToXml - Convert txg to an XML format.. */
 {
 struct txGraph *txg, *txgList = txGraphLoadAll(inTxg);
 verbose(1, "loaded %d from %s\n", slCount(txgList), inTxg);
 FILE *f = mustOpen(outXml, "w");
 fprintf(f, "<txGraphList count=\"%d\">\n", slCount(txgList));
 for (txg = txgList; txg != NULL; txg = txg->next)
     {
     txgWriteXml(txg, f);
     }
 fprintf(f, "</txGraphList>\n");
 carefulClose(&f);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 showEvidence = !optionExists("noEvidence");
 if (argc != 3)
     usage();
 txgToXml(argv[1], argv[2]);
 return 0;
 }