624f4b612627304cc2424be2d1ab7a314ab651a2
kent
  Tue May 27 10:43:34 2014 -0700
Adding spacing for readability around some copyrights notices that needed it.
diff --git src/lib/mafFromAxt.c src/lib/mafFromAxt.c
index 96c5f9f..c32546a 100644
--- src/lib/mafFromAxt.c
+++ src/lib/mafFromAxt.c
@@ -1,80 +1,81 @@
 /* mafFromAxt - convert a axt into maf. */
 
 /* Copyright (C) 2011 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
+
 #include "common.h"
 #include "axt.h"
 #include "maf.h"
 
 
 void mafFromAxtTemp(struct axt *axt, int tSize, int qSize,
 	struct mafAli *temp)
 /* Make a maf out of axt,  parasiting on the memory in axt.
  * Do *not* mafFree this temp.  The memory it has in pointers
  * is still owned by the axt.  Furthermore the next call to
  * this function will invalidate the previous temp value.
  * It's sort of a kludge, but quick to run and easy to implement. */
 {
 static struct mafComp qComp, tComp;
 ZeroVar(temp);
 ZeroVar(&qComp);
 ZeroVar(&tComp);
 temp->score = axt->score;
 temp->textSize = axt->symCount;
 qComp.src = axt->qName;
 qComp.srcSize = qSize;
 qComp.strand = axt->qStrand;
 qComp.start = axt->qStart;
 qComp.size = axt->qEnd - axt->qStart;
 qComp.text = axt->qSym;
 slAddHead(&temp->components, &qComp);
 tComp.src = axt->tName;
 tComp.srcSize = tSize;
 tComp.strand = axt->tStrand;
 tComp.start = axt->tStart;
 tComp.size = axt->tEnd - axt->tStart;
 tComp.text = axt->tSym;
 slAddHead(&temp->components, &tComp);
 }
 
 struct mafAli *mafFromAxt(struct axt *axt, int tSize, 
 	char *tPrefix, int qSize, char *qPrefix)
 /* Make up a maf file from axt.  Slower than mafFromAxtTemp,
  * but the axt and maf are independent afterwards. */
 {
 struct mafAli *maf;
 struct mafComp *mc;
 char name[256];
 AllocVar(maf);
 maf->score = axt->score;
 maf->textSize = axt->symCount;
 AllocVar(mc);
 if (qPrefix == NULL)
     mc->src = cloneString(axt->qName);
 else
     {
     safef(name, sizeof(name), "%s.%s", qPrefix, axt->qName);
     mc->src = cloneString(name);
     }
 mc->srcSize = qSize;
 mc->strand = axt->qStrand;
 mc->start = axt->qStart;
 mc->size = axt->qEnd - axt->qStart;
 mc->text = cloneStringZ(axt->qSym, axt->symCount);
 slAddHead(&maf->components, mc);
 AllocVar(mc);
 if (tPrefix == NULL)
     mc->src = cloneString(axt->tName);
 else
     {
     safef(name, sizeof(name), "%s.%s", tPrefix, axt->tName);
     mc->src = cloneString(name);
     }
 mc->srcSize = tSize;
 mc->strand = axt->tStrand;
 mc->start = axt->tStart;
 mc->size = axt->tEnd - axt->tStart;
 mc->text = cloneStringZ(axt->tSym, axt->symCount);
 slAddHead(&maf->components, mc);
 return maf;
 }