String BinaryResources::browseForResource (const String& title,
const String& wildcard,
const File& fileToStartFrom,
const String& resourceToReplace)
{
FileChooser fc (title, fileToStartFrom, wildcard);
if (fc.browseForFileToOpen())
{
String name (resourceToReplace);
if (name.isEmpty())
name = findUniqueName (fc.getResult().getFileName());
if (! add (name, fc.getResult()))
{
AlertWindow::showMessageBox (AlertWindow::WarningIcon,
TRANS("Adding Resource"),
TRANS("Failed to load the file!"));
name.clear();
}
return name;
}
return String::empty;
}
void genePredWriteToGtf(struct genePred *gp, char *source,
struct hash *dupeHash, FILE *f)
/* Write out genePredName to GTF file. */
{
int i;
char *name = findUniqueName(dupeHash, gp->name);
char *geneName = gp->name2;
char *chrom = gp->chrom;
char strand = gp->strand[0];
int *frames = (gp->optFields & genePredExonFramesFld) ? gp->exonFrames : calcFrames(gp);
struct codonCoords firstCodon = findFirstCodon(gp, frames);
struct codonCoords lastCodon = findLastCodon(gp, frames);
// figure out bounds of CDS and UTR regions, moving stop codon to outside of
// CDS.
int firstUtrEnd = gp->cdsStart, lastUtrStart = gp->cdsEnd;
int cdsStart = gp->cdsStart, cdsEnd = gp->cdsEnd;
if ((strand == '+') && codonComplete(&lastCodon))
cdsEnd = movePos(gp, lastUtrStart, -3);
if ((strand == '-') && codonComplete(&firstCodon))
cdsStart = movePos(gp, cdsStart, 3);
if (addComments)
fprintf(f, "###\n# %s %s:%d-%d (%s) CDS: %d-%d\n#\n",
gp->name, gp->chrom, gp->txStart, gp->txEnd,
gp->strand, gp->cdsStart, gp->cdsEnd);
for (i=0; i<gp->exonCount; ++i)
{
writeGtfLine(f, source, name, geneName, chrom, strand, "exon",
gp->exonStarts[i], gp->exonEnds[i], i, -1);
if (cdsStart < cdsEnd)
writeFeatures(gp, i, source, name, chrom, strand, geneName,
firstUtrEnd, cdsStart, cdsEnd, lastUtrStart,
frames[i], f);
}
if (gp->strand[0] == '+')
{
if (codonComplete(&firstCodon))
writeCodon(f, source, name, geneName, chrom, strand, "start_codon",
&firstCodon);
if (codonComplete(&lastCodon))
writeCodon(f, source, name, geneName, chrom, strand, "stop_codon",
&lastCodon);
}
else
{
if (codonComplete(&lastCodon))
writeCodon(f, source, name, geneName, chrom, strand, "start_codon",
&lastCodon);
if (codonComplete(&firstCodon))
writeCodon(f, source, name, geneName, chrom, strand, "stop_codon",
&firstCodon);
}
if (!(gp->optFields & genePredExonFramesFld))
freeMem(frames);
}
