inc/pslTransMap.h File Reference

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Enumerations
enum	pslTransMapOpts { pslTransMapNoOpts = 0x00, pslTransMapKeepTrans = 0x01 }
Functions
psl *	pslTransMap (unsigned opts, struct psl *inPsl, struct psl *mapPsl)

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Enumeration Type Documentation

enum pslTransMapOpts

Enumerator:

pslTransMapNoOpts
pslTransMapKeepTrans

Definition at line 6 of file pslTransMap.h.

{
    pslTransMapNoOpts     = 0x00,  /* no options */
    pslTransMapKeepTrans  = 0x01   /* keep translated alignment strand */
};

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Function Documentation

struct psl* pslTransMap	(	unsigned	opts,
		struct psl *	inPsl,
		struct psl *	mapPsl
	)			[read]

Definition at line 247 of file pslTransMap.c.

References adjustOrientation(), psl::blockCount, blockFromPslBlock(), createMappedPsl(), errAbort(), mapBlock(), pslFree(), pslIsProtein(), pslNAToProt(), pslProtToNA(), pslQStrand, pslRc(), pslTStrand, psl::qName, psl::qSize, safef(), sameString, setPslBounds(), psl::tName, and psl::tSize.

{
int mappedPslMax = 8; /* allocated space in output psl */
int iMapBlk = 0;
char inPslOrigStrand[3];
boolean rcInPsl = (pslTStrand(inPsl) != pslQStrand(mapPsl));
boolean cnv1 = (pslIsProtein(inPsl) && !pslIsProtein(mapPsl));
boolean cnv2 = (pslIsProtein(mapPsl) && !pslIsProtein(inPsl));
int iBlock;
struct psl* mappedPsl;

if (!sameString(inPsl->tName, mapPsl->qName))
    errAbort("Error: inPsl tName %s != mapPsl tName %s)",
            inPsl->tName, mapPsl->qName);
if (inPsl->tSize != mapPsl->qSize)
    errAbort("Error: inPsl %s tSize (%d) != mapPsl %s qSize (%d)",
            inPsl->tName, inPsl->tSize, mapPsl->qName, mapPsl->qSize);

/* convert protein PSLs */
if (cnv1)
    pslProtToNA(inPsl);
if (cnv2)
    pslProtToNA(mapPsl);

/* need to ensure common sequence is in same orientation, save strand for later */
safef(inPslOrigStrand, sizeof(inPslOrigStrand), "%s", inPsl->strand);
if (rcInPsl)
    pslRc(inPsl);

mappedPsl = createMappedPsl(inPsl, mapPsl, mappedPslMax);

/* Fill in ungapped blocks.  */
for (iBlock = 0; iBlock < inPsl->blockCount; iBlock++)
    {
    struct block align1Blk = blockFromPslBlock(inPsl, iBlock);
    while (mapBlock(inPsl, mapPsl, &iMapBlk, &align1Blk, mappedPsl,
                    &mappedPslMax))
        continue;
    }

/* finish up psl, or free if no blocks were added */
assert(mappedPsl->blockCount <= mappedPslMax);
if (mappedPsl->blockCount == 0)
    pslFree(&mappedPsl);  /* nothing made it */
else
    {
    setPslBounds(mappedPsl);
    adjustOrientation(opts, inPsl, inPslOrigStrand, mappedPsl);
    }

/* restore input */
if (rcInPsl)
    {
    pslRc(inPsl);
    strcpy(inPsl->strand, inPslOrigStrand);
    }
if (cnv1)
    pslNAToProt(inPsl);
if (cnv2)
    pslNAToProt(mapPsl);

return mappedPsl;
}

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