Esempio n. 1
0
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));
	}
}
Esempio n. 2
0
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
}