void addChainT(struct chrom *chrom, struct chrom *otherChrom, struct chain *chain)
/* Add T side of chain to fill/gap tree of chromosome.
* This is the easier case since there are no strand
* issues to worry about. */
{
struct slRef *spaceList;
struct slRef *ref;
struct cBlock *startBlock, *block, *nextBlock;
struct gap *gap;
spaceList = findSpaces(chrom->spaces,chain->tStart,chain->tEnd);
startBlock = chain->blockList;
for (ref = spaceList; ref != NULL; ref = ref->next)
{
struct space *space = ref->val;
struct fill *fill;
int gapStart, gapEnd;
for (;;)
{
nextBlock = startBlock->next;
if (nextBlock == NULL)
break;
gapEnd = nextBlock->tStart;
if (gapEnd > space->start)
break;
startBlock = nextBlock;
}
if ((fill = fillSpace(chrom, space, chain, startBlock, FALSE)) != NULL)
{
for (block = startBlock; ; block = nextBlock)
{
nextBlock = block->next;
if (nextBlock == NULL)
break;
gapStart = block->tEnd;
gapEnd = nextBlock->tStart;
if (strictlyInside(space->start, space->end, gapStart, gapEnd))
{
int qs = block->qEnd;
int qe = nextBlock->qStart;
if (chain->qStrand == '-')
reverseIntRange(&qs, &qe, chain->qSize);
gap = gapNew(gapStart, gapEnd, qs, qe);
addSpaceForGap(chrom, gap);
slAddHead(&fill->gapList, gap);
}
}
freez(&ref->val); /* aka space */
}
}
slFreeList(&spaceList);
}
int main(int argc, char * argv[])
{
if(argc < 2)
{
printf("Usage: %s <string>\n", argv[0]);
return(EXIT_FAILURE);
}
int lengthOld = strlen(argv[1]);
int lengthNew;
char * newString;
char * oldString;
oldString = malloc(sizeof(char) * (lengthOld + 1));
strncpy(oldString, argv[1], lengthOld);
oldString[lengthOld] = '\0';
lengthNew = lengthOld + (2 * findSpaces(oldString));
newString = malloc(sizeof(char) * (lengthNew + 1));
newString[lengthNew] = '\0';
printf("Old String: %s\n", oldString);
replaceSpaces(oldString, newString, lengthOld, lengthNew);
printf("New String: %s\n", newString);
free(oldString);
free(newString);
return(EXIT_SUCCESS);
}
void addChainQ(struct chrom *chrom, struct chrom *otherChrom, struct chain *chain)
/* Add Q side of chain to fill/gap tree of chromosome.
* For this side we have to cope with reverse strand
* issues. */
{
struct slRef *spaceList;
struct slRef *ref;
struct cBlock *startBlock, *block, *nextBlock;
int gapStart, gapEnd;
struct gap *gap;
boolean isRev = (chain->qStrand == '-');
int qStart = chain->qStart, qEnd = chain->qEnd;
if (isRev)
{
reverseIntRange(&qStart, &qEnd, chain->qSize);
reverseBlocksQ(&chain->blockList, chain->qSize);
}
spaceList = findSpaces(chrom->spaces,qStart,qEnd);
startBlock = chain->blockList;
for (ref = spaceList; ref != NULL; ref = ref->next)
{
struct space *space = ref->val;
struct fill *fill;
for (;;)
{
nextBlock = startBlock->next;
if (nextBlock == NULL)
break;
gapEnd = nextBlock->qStart;
if (gapEnd > space->start)
break;
startBlock = nextBlock;
}
if ((fill = fillSpace(chrom, space, chain, startBlock, TRUE))
!= NULL)
{
for (block = startBlock; ; block = nextBlock)
{
nextBlock = block->next;
if (nextBlock == NULL)
break;
gapStart = block->qEnd;
gapEnd = nextBlock->qStart;
if (strictlyInside(space->start, space->end, gapStart, gapEnd))
{
int ts, te;
if (chain->qStrand == '+')
{
ts = block->tEnd;
te = nextBlock->tStart;
}
else
{
ts = nextBlock->tStart;
te = block->tEnd;
}
gap = gapNew(gapStart, gapEnd, ts, te);
addSpaceForGap(chrom, gap);
slAddHead(&fill->gapList, gap);
}
}
freez(&ref->val); /* aka space */
}
}
slFreeList(&spaceList);
if (isRev)
reverseBlocksQ(&chain->blockList, chain->qSize);
}
