ed6faffdb401ee2cf58b4f796a6b8ee8e75c7577
kent
  Tue May 27 10:45:12 2014 -0700
Adding spacing for readability around some copyrights notices that needed it.
diff --git src/lib/xenshow.c src/lib/xenshow.c
index 8b1bc08..c776c72 100644
--- src/lib/xenshow.c
+++ src/lib/xenshow.c
@@ -1,64 +1,65 @@
 /* xenshow - show a cross-species alignment. 
  *
  * This file is copyright 2002 Jim Kent, but license is hereby
  * granted for all use - public, private or commercial. */
+
 #include "common.h"
 #include "nt4.h"
 #include "xenalign.h"
 
 
 static void printMatchers(char *a, char *b, int lineSize, FILE *f)
 /* Print '|' where a[i] and b[i] match, ' ' where they don't */
 {
 int i;
 for (i=0; i<lineSize; ++i)
    {
    char c = ((a[i] == b[i]) ? '|' : ' ');
    fputc(c, f);
    }
 }
 
 static int nonDashCount(char *s, int size)
 /* Return number of characters in s[0] to s[size-1] that
  * aren't dashes. */
 {
 int count = 0;
 int i;
 for (i=0; i<size; ++i)
     if (s[i] != '-')
         ++count;
 return count;
 }
 
 void xenShowAli(char *qSym, char *tSym, char *hSym, int symCount, FILE *f,
    int qOffset, int tOffset, char qStrand, char tStrand, int maxLineSize)
 /* Print alignment and HMM symbols maxLineSize bases at a time to file. */
 {
 int i;
 int lineSize;
 int count;
 
 for (i=0; i<symCount; i += lineSize)
     {
     lineSize = symCount - i;
     if (lineSize > maxLineSize) lineSize = maxLineSize;
     mustWrite(f, qSym+i, lineSize);
     count = nonDashCount(qSym+i, lineSize);
     if (qStrand == '-')
         count = -count;
     qOffset += count;
     fprintf(f, " %9d\n", qOffset);
     printMatchers(qSym+i, tSym+i, lineSize, f);
     fputc('\n', f);
     mustWrite(f, tSym+i, lineSize);
     count = nonDashCount(tSym+i, lineSize);
     if (tStrand == '-')
         count = -count;
     tOffset += count;
     fprintf(f, " %9d\n", tOffset);
     mustWrite(f, hSym+i, lineSize);
     fputc('\n', f);
     fputc('\n', f);
     }
 }