void LC_MakerCamSVG::writeEntity(RS_Entity* entity) {
RS_DEBUG->print("RS_MakerCamSVG::writeEntity: Found entity ...");
switch (entity->rtti()) {
case RS2::EntityInsert:
writeInsert((RS_Insert*)entity);
break;
case RS2::EntityPoint:
writePoint((RS_Point*)entity);
break;
case RS2::EntityLine:
writeLine((RS_Line*)entity);
break;
case RS2::EntityPolyline:
writePolyline((RS_Polyline*)entity);
break;
case RS2::EntityCircle:
writeCircle((RS_Circle*)entity);
break;
case RS2::EntityArc:
writeArc((RS_Arc*)entity);
break;
case RS2::EntityEllipse:
writeEllipse((RS_Ellipse*)entity);
break;
default:
RS_DEBUG->print("RS_MakerCamSVG::writeEntity: Entity with type '%d' not yet implemented",
(int)entity->rtti());
break;
}
}
struct axt *pslToAxt(struct psl *psl, struct hash *qHash, char *tNibDir,
struct dlList *fileCache)
{
static char *tName = NULL, *qName = NULL;
static struct dnaSeq *tSeq = NULL;
struct dyString *q = newDyString(16*1024);
struct dyString *t = newDyString(16*1024);
int blockIx;
int qs, ts ;
int lastQ = 0, lastT = 0, size;
int qOffset = 0;
int tOffset = 0;
struct axt *axt = NULL;
boolean qIsNib = FALSE;
boolean tIsNib = FALSE;
int cnt = 0;
//struct dnaSeq *tSeq = NULL;
struct nibInfo *tNib = NULL;
struct dnaSeq *qSeq = twoBitReadSeqFrag(twoBitFile, psl->qName, 0, 0);
// hGenBankGetMrna(psl->qName, NULL);
/*
freeDnaSeq(&qSeq);
freez(&qName);
assert(mrnaList != NULL);
for (mrna = mrnaList; mrna != NULL ; mrna = mrna->next)
{
assert(mrna != NULL);
cnt++;
if (sameString(mrna->name, psl->qName))
{
qSeq = cloneDnaSeq(mrna);
assert(qSeq != NULL);
break;
}
}
*/
if (qSeq == NULL)
{
warn("mrna sequence data not found %s, searched %d sequences\n",psl->qName,cnt);
dyStringFree(&q);
dyStringFree(&t);
dnaSeqFree(&tSeq);
dnaSeqFree(&qSeq);
return NULL;
}
if (qSeq->size != psl->qSize)
{
warn("sequence %s aligned is different size %d from mrna.fa file %d \n",psl->qName,psl->qSize,qSeq->size);
dyStringFree(&q);
dyStringFree(&t);
dnaSeqFree(&tSeq);
dnaSeqFree(&qSeq);
return NULL;
}
qName = cloneString(psl->qName);
if (qIsNib && psl->strand[0] == '-')
qOffset = psl->qSize - psl->qEnd;
else
qOffset = 0;
verbose(5,"qString len = %d qOffset = %d\n",qSeq->size,qOffset);
if (tName == NULL || !sameString(tName, psl->tName) || tIsNib)
{
freeDnaSeq(&tSeq);
freez(&tName);
tName = cloneString(psl->tName);
tNib = nibInfoFromCache(nibHash, tNibDir, tName);
assert(tNib !=NULL);
tSeq = nibInfoLoadStrand(tNib, psl->tStart, psl->tEnd, '+');
assert(tSeq !=NULL);
tOffset = psl->tStart;
//readCachedSeqPart(tName, psl->tStart, psl->tEnd-psl->tStart,
// tHash, fileCache, &tSeq, &tOffset, &tIsNib);
}
verbose(4,"strand t %s \n",psl->strand);
if (tSeq != NULL)
verbose(5,"tString len = %d tOffset = %d\n",tSeq->size,tOffset);
else
errAbort("tSeq is NULL\n");
if (psl->strand[0] == '-')
reverseComplement(qSeq->dna, qSeq->size);
//if (strlen(psl->strand) > 1 )
// if (psl->strand[1] == '-')
// reverseComplement(tSeq->dna, tSeq->size);
for (blockIx=0; blockIx < psl->blockCount; ++blockIx)
{
qs = psl->qStarts[blockIx] - qOffset;
ts = psl->tStarts[blockIx] - tOffset;
if (blockIx != 0)
{
int qGap, tGap, minGap;
qGap = qs - lastQ;
tGap = ts - lastT;
minGap = min(qGap, tGap);
if (minGap > 0)
{
writeGap(q, qGap, qSeq->dna + lastQ, t, tGap, tSeq->dna + lastT);
}
else if (qGap > 0)
{
writeInsert(q, t, qSeq->dna + lastQ, qGap);
}
else if (tGap > 0)
{
writeInsert(t, q, tSeq->dna + lastT, tGap);
}
}
size = psl->blockSizes[blockIx];
assert(qSeq != NULL);
dyStringAppendN(q, qSeq->dna + qs, size);
lastQ = qs + size;
dyStringAppendN(t, tSeq->dna + ts, size);
lastT = ts + size;
}
if (strlen(q->string) != strlen(t->string))
warn("Symbol count(t) %d != %d inconsistent at t %s:%d and qName %s\n%s\n%s\n",
(int)strlen(t->string), (int)strlen(q->string), psl->tName, psl->tStart, psl->qName, t->string, q->string);
if (psl->strand[0] == '-')
{
reverseComplement(q->string, q->stringSize);
reverseComplement(t->string, t->stringSize);
}
axt = axtCreate(q->string, t->string, min(q->stringSize,t->stringSize), psl);
dyStringFree(&q);
dyStringFree(&t);
//dnaSeqFree(&tSeq);
dnaSeqFree(&qSeq);
if (qIsNib)
freez(&qName);
//if (tIsNib)
// freez(&tName);
return axt;
}
void prettyOne(struct psl *psl, struct hash *qHash, struct hash *tHash,
struct dlList *fileCache, FILE *f, boolean axt, FILE *checkFile)
/* Make pretty output for one psl. Find target and query
* sequence in hash. Load them. Output bases. */
{
static char *tName = NULL, *qName = NULL;
static struct dnaSeq *tSeq = NULL, *qSeq = NULL;
struct dyString *q = newDyString(16*1024);
struct dyString *t = newDyString(16*1024);
int blockIx;
int qs, ts;
int lastQ = 0, lastT = 0, size;
int qOffset = 0;
int tOffset = 0;
boolean qIsPartial = FALSE;
boolean tIsPartial = FALSE;
if (qName == NULL || !sameString(qName, psl->qName))
{
freeDnaSeq(&qSeq);
freez(&qName);
qName = cloneString(psl->qName);
readCachedSeqPart(qName, psl->qStart, psl->qEnd-psl->qStart,
qHash, fileCache, &qSeq, &qOffset, &qIsPartial);
if (qIsPartial && psl->strand[0] == '-')
qOffset = psl->qSize - psl->qEnd;
}
if (tName == NULL || !sameString(tName, psl->tName) || tIsPartial)
{
freeDnaSeq(&tSeq);
freez(&tName);
tName = cloneString(psl->tName);
readCachedSeqPart(tName, psl->tStart, psl->tEnd-psl->tStart,
tHash, fileCache, &tSeq, &tOffset, &tIsPartial);
}
if (tIsPartial && psl->strand[1] == '-')
tOffset = psl->tSize - psl->tEnd;
if (psl->strand[0] == '-')
reverseComplement(qSeq->dna, qSeq->size);
if (psl->strand[1] == '-')
reverseComplement(tSeq->dna, tSeq->size);
for (blockIx=0; blockIx < psl->blockCount; ++blockIx)
{
qs = psl->qStarts[blockIx] - qOffset;
ts = psl->tStarts[blockIx] - tOffset;
/* Output gaps except in first case. */
if (blockIx != 0)
{
int qGap, tGap, minGap;
qGap = qs - lastQ;
tGap = ts - lastT;
minGap = min(qGap, tGap);
if (minGap > 0)
{
writeGap(q, qGap, qSeq->dna + lastQ, t, tGap, tSeq->dna + lastT);
}
else if (qGap > 0)
{
writeInsert(q, t, qSeq->dna + lastQ, qGap);
}
else if (tGap > 0)
{
writeInsert(t, q, tSeq->dna + lastT, tGap);
}
}
/* Output sequence. */
size = psl->blockSizes[blockIx];
dyStringAppendN(q, qSeq->dna + qs, size);
lastQ = qs + size;
dyStringAppendN(t, tSeq->dna + ts, size);
lastT = ts + size;
if(q->stringSize != t->stringSize)
{
// printf("%d BLK %s q size %d t size %d diff %d qs size %d ts size %d\n",blockIx, psl->qName, q->stringSize, t->stringSize, q->stringSize - t->stringSize, qSeq->size, tSeq->size );
}
}
if (checkFile != NULL)
{
outputCheck(psl, qSeq, qOffset, tSeq, tOffset, checkFile);
}
if (psl->strand[0] == '-' && !qIsPartial)
reverseComplement(qSeq->dna, qSeq->size);
if (psl->strand[1] == '-' && !tIsPartial)
reverseComplement(tSeq->dna, tSeq->size);
if(q->stringSize != t->stringSize)
{
// printf("AF %s q size %d t size %d qs size %d ts size %d\n",psl->qName, q->stringSize, t->stringSize, qSeq->size, tSeq->size );
}
//assert(q->stringSize == t->stringSize);
if (axt)
axtOutString(q->string, t->string, min(q->stringSize,t->stringSize), 60, psl, f);
else
prettyOutString(q->string, t->string, min(q->stringSize,t->stringSize), 60, psl, f);
dyStringFree(&q);
dyStringFree(&t);
if (qIsPartial)
freez(&qName);
if (tIsPartial)
freez(&tName);
}
