static void
pseudoflowPhase1 (void)
{
Node *strongRoot;
int theparam = 0;
double thetime;
thetime = timer ();
while ((strongRoot = getHighestStrongRoot (theparam)))
{
processRoot (strongRoot);
}
printf ("c Finished solving parameter %d\nc Flow: %d\nc Elapsed time: %.3f\n",
(theparam+1),
computeMinCut (),
(timer () - thetime));
for (theparam=1; theparam < numParams; ++ theparam)
{
updateCapacities (theparam);
#ifdef PROGRESS
printf ("c Finished updating capacities and excesses.\n");
fflush (stdout);
#endif
while ((strongRoot = getHighestStrongRoot (theparam)))
{
processRoot (strongRoot);
}
printf ("c Finished parameter: %d\nc Flow: %d\nc Elapsed time: %.3f\n",
(theparam+1),
computeMinCut (),
(timer () - thetime));
}
}
static void gff3ToPsl(char *mapFile, char *inGff3File, char *outPSL)
/* gff3ToPsl - convert a GFF3 file to a genePred file. */
{
struct hash *chromHash = readSizes(mapFile);
struct hash *processed = hashNew(12);
struct gff3File *gff3File = loadGff3(inGff3File);
FILE *pslF = mustOpen(outPSL, "w");
struct gff3AnnRef *root;
for (root = gff3File->roots; root != NULL; root = root->next)
{
if (!isProcessed(processed, root->ann))
{
processRoot(pslF, root->ann, processed, chromHash);
if (convertErrCnt >= maxConvertErrs)
break;
}
}
carefulClose(&pslF);
if (convertErrCnt > 0)
errAbort("%d errors converting GFF3 file: %s", convertErrCnt, inGff3File);
#if 0 // free memory for leak debugging if 1
gff3FileFree(&gff3File);
hashFree(&processed);
#endif
}
