Fixed a serious bug in DynamicPersistenceTrails + LSVineyard sorts filtration by attachment + miscellanea:
* added program options to pdbdistance-vineyard
* pdbdistance-vineyard takes frame list in a file
* more logging
* verification of pairing after vertex transpositions (commented out)
#include <utilities/counter.h>
static Counter* cTestElaborate = GetCounter("test/elaborate");
static Counter* cTestBasic = GetCounter("test/basic");
static Counter* cTestBasicSub = GetCounter("test/basic/sub");
int main()
{
SetFrequency(cTestBasic, 2);
Count(cTestBasic);
Count(cTestBasicSub);
Count(cTestBasicSub);
Count(cTestBasicSub);
Count(cTestElaborate);
Count(cTestBasic);
Count(cTestElaborate);
Count(cTestBasic);
Count(cTestBasic);
CountNum(cTestBasic, 25);
CountNum(cTestBasic, 132);
CountNum(cTestBasic, 25);
CountNum(cTestBasic, 121);
CountNum(cTestBasic, 132);
CountNum(cTestBasic, 25);
SetTrigger(cTestBasic, &rootCounter);
Count(cTestBasic);
Count(cTestBasic);
SetFrequency(cTestElaborate, 3);
Count(cTestElaborate);
}