e70152e44cc66cc599ff6b699eb8adc07f3e656a
kent
  Sat May 24 21:09:34 2014 -0700
Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
diff --git src/hg/lib/axtLib.c src/hg/lib/axtLib.c
index 239348d..1cd5fff 100644
--- src/hg/lib/axtLib.c
+++ src/hg/lib/axtLib.c
@@ -1,189 +1,192 @@
 /* axtLib - Convert chain to axt */
+
+/* Copyright (C) 2014 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "chainBlock.h"
 #include "dnautil.h"
 #include "dnaseq.h"
 #include "chainNet.h"
 #include "nib.h"
 #include "axt.h"
 #include "axtLib.h"
 #include "axtInfo.h"
 #include "chainToAxt.h"
 #include "hdb.h"
 
 
 
 struct axt *netFillToAxt(struct cnFill *fill, struct dnaSeq *tChrom , int tSize,
 	struct hash *qChromHash, char *nibDir,
 	struct chain *chain, boolean swap)
 /* Convert subset of chain as defined by fill to axt. swap query and target if swap is true*/
 {
 struct dnaSeq *qSeq;
 boolean isRev = (chain->qStrand == '-');
 struct chain *subChain, *chainToFree;
 int qOffset;
 struct axt *axtList = NULL , *axt;
 struct nibInfo *nib = hashFindVal(qChromHash, fill->qName);
 
 /* Get query sequence fragment. */
     {
     if (nib == NULL)
         {
 	char path[512];
 	AllocVar(nib);
 	safef(path, sizeof(path), "%s/%s.nib", nibDir, fill->qName);
 	nib->fileName = cloneString(path);
 	nibOpenVerify(path, &nib->f, &nib->size);
 	hashAdd(qChromHash, fill->qName, nib);
 	}
     qSeq = nibLoadPartMasked(NIB_MASK_MIXED, nib->fileName, 
     	fill->qStart, fill->qSize);
     if (isRev)
 	{
         reverseComplement(qSeq->dna, qSeq->size);
 	qOffset = nib->size - (fill->qStart + fill->qSize);
 	}
     else
 	qOffset = fill->qStart;
     }
 chainSubsetOnT(chain, fill->tStart, fill->tStart + fill->tSize, 
 	&subChain, &chainToFree);
 if (subChain != NULL)
     {
     axtList = chainToAxt(subChain, qSeq, qOffset, tChrom, fill->tStart, 100, BIGNUM);
     if (swap)
         {
         for (axt = axtList ; axt != NULL ; axt = axt->next)
             axtSwap(axt, tSize, nib->size);
         }
     }
 chainFree(&chainToFree);
 freeDnaSeq(&qSeq);
 return axtList;
 }
 
 void axtListReverse(struct axt **axtList, char *queryDb)
 /* reverse complement an entire axtList */
 {
 struct axt *axt;
 int tmp;
 
 for (axt = *axtList; axt != NULL; axt = axt->next)
     {
     int qSize = 0;
         
     if (sameString(axt->qName , "gap"))
         qSize = axt->qEnd;
     else
         qSize = hChromSize(queryDb, axt->qName);
 
     reverseComplement(axt->qSym, axt->symCount);
     reverseComplement(axt->tSym, axt->symCount);
     tmp = qSize - axt->qStart;
     axt->qStart = qSize - axt->qEnd;
     axt->qEnd = tmp;
     }
 slReverse(axtList);
 }
 
 struct axt *createAxtGap(char *nibFile, char *chrom, 	
 			 int start, int end, char strand)
 /* return an axt alignment with the query all deletes - null aligment */
 {
 struct axt *axt;
 int size = end-start;
 char *gapPt = needLargeMem(size+1);
 char *p;
 struct dnaSeq *seq = NULL;
 
 for (p=gapPt;p<=gapPt+size;p++)
     *p = '-';
 AllocVar(axt);
 axt->tName = chrom;
 axt->tStart = start;
 axt->tEnd = end;
 axt->tStrand = strand;
 axt->qName = "gap";
 axt->qStart = 1;
 axt->qEnd = size;
 axt->qStrand = strand;
 axt->symCount = size;
 axt->score = 0;
 seq = nibLoadPart(nibFile, start,size);
 axt->tSym = cloneMem(seq->dna, size+1);
 axt->qSym = cloneMem(gapPt, size+1);
 return axt;
 }
 
 void axtFillGap(struct axt **aList, char *nibDir, char direction)
 /* fill gaps between blocks with null axts with seq on t and q seq all gaps*/
 /* direction = '+' ascending on + strand, - is descending on - strand */
 {
 struct axt *axt, *next, *axtGap, *tmp, *prevAxt = NULL;
 int prevEnd = 0;
 int prevStart = 0;
 char nib[128];
 
 for (axt = *aList; axt != NULL; axt = next)
     {
     if (((axt->tStart)-1) > prevEnd  && prevEnd > 0 && direction == '+')
         {
         assert(prevAxt != NULL);
         tmp = prevAxt->next;
         safef(nib, sizeof(nib), "%s/%s.nib",nibDir,axt->tName);
         axtGap = createAxtGap(nib,axt->tName,prevEnd,(axt->tStart),axt->qStrand);
         axtGap->next = tmp;
         prevAxt->next = axtGap;
         }
     if (((axt->tEnd)+1) < prevStart  && prevStart > 0 && direction == '-')
         {
         assert(prevAxt != NULL);
         tmp = prevAxt->next;
         safef(nib, sizeof(nib), "%s/%s.nib",nibDir,axt->tName);
         axtGap = createAxtGap(nib,axt->tName,(axt->tEnd),prevStart,axt->qStrand);
         axtGap->next = tmp;
         prevAxt->next = axtGap;
         }
     prevEnd = axt->tEnd;
     prevStart = axt->tStart;
     prevAxt = axt;
     next = axt->next;
     }
 }
 char *getAxtFileName(char *chrom, char *toDb, char *alignment, char *fromDb)
 /* return file name for a axt alignment */
 {
 char query[256];
 struct sqlResult *sr;
 struct sqlConnection *conn = hAllocConn(fromDb);
 char **row;
 struct axtInfo *ai = NULL;
 
 if (alignment != NULL)
     sqlSafef(query, sizeof(query),
 	     "select * from axtInfo where chrom = '%s' and species = '%s' and alignment = '%s'",
 	     chrom, toDb, alignment);
 else
     sqlSafef(query, sizeof(query),
 	     "select * from axtInfo where chrom = '%s' and species = '%s'",
 	     chrom, toDb);
 sr = sqlGetResult(conn, query);
 if ((row = sqlNextRow(sr)) != NULL)
     {
     ai = axtInfoLoad(row );
     }
 if (ai == NULL)
     {
     printf("\nNo alignments available for %s (database %s).\n\n",
 	   hFreezeFromDb(toDb), toDb);
     axtInfoFree(&ai);
     return NULL;
     }
 //axtInfoFree(&ai);
 return cloneString(ai->fileName);
 }