/* output a particular species sequence to the file stream */
void writeOutSpecies(FILE *f, char *dbName, struct speciesInfo *si,
struct exonInfo *giList)
{
if (inExons)
{
if (noTrans)
outSpeciesExonsNoTrans(f, dbName, si, giList);
else
outSpeciesExons(f, dbName, si, giList);
return;
}
struct exonInfo *lastGi;
//int start = giList->chromStart + 1;
for(lastGi = giList; lastGi->next ; lastGi = lastGi->next)
;
//int end = lastGi->chromEnd;
if (noTrans)
{
for(; si ; si = si->next)
{
if (!allDashes(si->nucSequence))
{
//fprintf(f, ">%s_%s %d %s.%s:%d-%d %c",
fprintf(f, ">%s_%s %d %s",
giList->name, si->name, si->size, allPos(si));
//dbName,
//giList->frame->chrom, start, end, giList->frame->strand[0]);
maybePrintGeneName(giList->name, f);
fprintf(f, "\n%s\n", si->nucSequence);
}
}
fprintf(f, "\n\n");
}
else
{
for(; si ; si = si->next)
{
translateProtein(si);
if (!allDashes(si->aaSequence))
{
//fprintf(f, ">%s_%s %d %s.%s:%d-%d %c",
fprintf(f, ">%s_%s %d %s",
giList->name, si->name, si->aaSize, allPos(si));
//dbName,
//giList->frame->chrom, start, end, giList->frame->strand[0]);
maybePrintGeneName(giList->name, f);
fprintf(f, "\n%s\n", si->aaSequence);
}
}
fprintf(f, "\n\n");
}
}
std::vector<int> Controller::calculatePositions(double t)
{
double angle, offset, amp, wav;
vector<int> allPos(d->getNumMotors(),-1);
for (unsigned int i = 0; i < d->getNumMotors(); i++) {
if (i%2==0) // n odd (n = i + 1, since i is 0-indexed)
{
offset = p->manualoffset ? p->offset[i] : p->masteroffsetOdd;
amp = p->manualamplitude ? p->amplitude[i] : p->amplitudeOdd;
wav = p->wavelengthOdd;
if (p->wavelengthOdd == 0)
wav = 1;
angle = (offset + amp*sin(2*PI*(p->frequencyOdd*t + i/wav)))*PI;
}
else
{
offset = p->manualoffset ? p->offset[i] : p->masteroffsetEven;
amp = p->manualamplitude ? p->amplitude[i] : p->amplitudeEven;
wav = p->wavelengthEven;
if (p->wavelengthEven == 0)
wav = 1;
angle = (offset + amp*sin(PI*(2*(p->frequencyEven*t + i/wav) + (p->phaseEven-p->phaseOdd))))*PI;
}
if (angle > PI/2)
angle = PI/2;
else if (angle < -PI/2)
angle = -PI/2;
allPos[i] = angle2Position(angle,d->getModel(i),true);
}
return allPos;
}
Aggregate ET::anything(Aggregate s,AggregateOrdered positions){
Word n=positions.elements();
return n==0 ? allPos(s,n) : allPos(s,positions[0]);
}
/* output a particular species sequence to the file stream */
static void writeOutSpecies(FILE *f, char *dbName, struct speciesInfo *si,
struct exonInfo *giList, unsigned options, int numCols)
{
boolean inExons = options & MAFGENE_EXONS;
boolean noTrans = options & MAFGENE_NOTRANS;
boolean doBlank = options & MAFGENE_OUTBLANK;
boolean doTable = options & MAFGENE_OUTTABLE;
if (inExons)
{
if (noTrans)
outSpeciesExonsNoTrans(f, dbName, si, giList, doBlank,
doTable, numCols);
else
outSpeciesExons(f, dbName, si, giList, doBlank, doTable, numCols);
return;
}
struct exonInfo *lastGi;
for(lastGi = giList; lastGi->next ; lastGi = lastGi->next)
;
if (noTrans)
{
for(; si ; si = si->next)
{
if (doBlank || !allDashes(si->nucSequence))
{
char buffer[10 * 1024];
safef(buffer, sizeof buffer, "%s_%s %d %s",
giList->name, si->name, si->size, allPos(si));
if (doTable)
{
if (numCols == -1)
fprintf(f, "%s ", buffer);
else
{
if (strlen(buffer) > numCols)
buffer[numCols] = 0;
fprintf(f, "%-*s ", numCols, buffer);
}
}
else
fprintf(f, ">%s\n", buffer);
fprintf(f, "%s\n", si->nucSequence);
}
}
fprintf(f, "\n\n");
}
else
{
for(; si ; si = si->next)
{
translateProtein(si);
char buffer[10 * 1024];
safef(buffer, sizeof buffer, "%s_%s %d %s",
giList->name, si->name, si->aaSize, allPos(si));
if (doBlank || !allDashes(si->aaSequence))
{
if (doTable)
{
if (numCols == -1)
fprintf(f, "%s ", buffer);
else
{
if (strlen(buffer) > numCols)
buffer[numCols] = 0;
fprintf(f, "%-*s ", numCols, buffer);
}
}
else
fprintf(f, ">%s\n", buffer);
fprintf(f, "%s\n", si->aaSequence);
}
}
fprintf(f, "\n\n");
}
}