C++ (Cpp) pslGrow示例

示例#1

文件： pslTransMap.c 项目： CRG-Barcelona/libbeato

static void addPslBlock(struct psl* psl, struct block* blk, int* pslMax)
/* add a block to a psl */
{
unsigned newIBlk = psl->blockCount;

assert((blk->qEnd - blk->qStart) == (blk->tEnd - blk->tStart));
if (newIBlk >= *pslMax)
    pslGrow(psl, pslMax);
psl->qStarts[newIBlk] = blk->qStart;
psl->tStarts[newIBlk] = blk->tStart;
psl->blockSizes[newIBlk] = blk->qEnd - blk->qStart;
/* lie about match counts. */
psl->match += psl->blockSizes[newIBlk];
/* count gaps */
if (newIBlk > 0)
    {
    if (psl->qStarts[newIBlk] > pslQEnd(psl, newIBlk-1))
        {
        psl->qNumInsert++;
        psl->qBaseInsert += psl->qStarts[newIBlk] - pslQEnd(psl, newIBlk-1);
        }
    if (psl->tStarts[newIBlk] > pslTEnd(psl, newIBlk-1))
        {
        psl->tNumInsert++;
        psl->tBaseInsert += psl->tStarts[newIBlk] - pslTEnd(psl, newIBlk-1);
        }
    }
psl->blockCount++;
}

示例#2

文件： pslBuild.c 项目： bowhan/kent

static void addUngappedBlock(struct psl* psl, int* pslSpace, struct block* blk, unsigned flags)
/* add the next  ungapped block to a psl */
{
unsigned newIBlk = psl->blockCount;
unsigned blkSize = blk->qEnd - blk->qStart;  // uses query size so protein psl is right
if (newIBlk >= *pslSpace)
    pslGrow(psl, pslSpace);
psl->qStarts[newIBlk] = blk->qCoordMult * blk->qStart;
psl->tStarts[newIBlk] = blk->tCoordMult * blk->tStart;
psl->blockSizes[newIBlk] = blk->qCoordMult * blkSize;

/* keep bounds current */
psl->qStart = psl->qStarts[0];
psl->qEnd = psl->qStarts[newIBlk] + (blk->qCoordMult * blkSize);
if (psl->strand[0] == '-')
    reverseIntRange(&psl->qStart, &psl->qEnd, psl->qSize);
psl->tStart = psl->tStarts[0];
psl->tEnd = psl->tStarts[newIBlk] + (blk->q2tBlkSizeMult * blkSize);
if (psl->strand[1] == '-')
    reverseIntRange(&psl->tStart, &psl->tEnd, psl->tSize);

if (flags & bldPslx)
    {
    psl->qSequence[newIBlk] = cloneStringZ(blk->qAln + blk->alnStart, blkSize);
    psl->tSequence[newIBlk] = cloneStringZ(blk->tAln + blk->alnStart, blkSize);
    }
psl->blockCount++;
}

示例#3

文件： pslTransMap.c 项目： Puneet-Shivanand/zinba

static void addPslBlock(struct psl* psl, struct block* blk, int* pslMax)
/* add a block to a psl */
{
unsigned newIBlk = psl->blockCount;

assert((blk->qEnd - blk->qStart) == (blk->tEnd - blk->tStart));
if (newIBlk >= *pslMax)
    pslGrow(psl, pslMax);
psl->qStarts[newIBlk] = blk->qStart;
psl->tStarts[newIBlk] = blk->tStart;
psl->blockSizes[newIBlk] = blk->qEnd - blk->qStart;
/* lie about match counts. */
psl->match += psl->blockSizes[newIBlk];
psl->blockCount++;
}