int main (int argc, char **argv)
{
int inputFormat = IF_NEXUS;
int outputFormat = OF_STANDARD;
if (argc > 2)
{
for (int i=2;i<argc;i++)
{
//cout << argv[i];
string tempString = argv[i];
if (tempString == "-p")
{
inputFormat = IF_PHYLIP;
outputFormat = OF_PHYLIP;
}
}
}
else {
cout << "Need size of bootstrap columns. " << endl;
exit(0);
}
// First argument is the bootstrap size.
int numCols = atoi(argv[1]);
int randomSeed = time(0);
// Second argument is the random seed.
if (argc > 3)
{
randomSeed = atoi(argv[2]);
}
srand(randomSeed);
Alignment myalign;
myalign.setInputFormat(inputFormat);
cin >> myalign;
//cout << myalign;
//myalign.setOutputFormat(OF_NEXUS);
//cout << myalign;
//myalign.setOutputFormat(OF_PHYLIP);
//cout << myalign;
//cout.precision(10);
//cout << "Min: " << myalign.sequenceDivergenceMin() << endl;
//cout << "Avg: " << myalign.sequenceDivergenceAvg() << endl;
//myalign.printSequenceDivergencePairs();
Alignment bootstrapAlign = myalign.getBootstrap(1, numCols);
bootstrapAlign.setOutputFormat(outputFormat);
cout << bootstrapAlign;
}
int main (int argc, char **argv)
{
if (argc > 1 ) {
string tmpStr = argv[1];
if (tmpStr == "-v") {
DEBUG_OUTPUT = 3;
}
}
Alignment myalign;
cin >> myalign;
myalign.setOutputFormat(OF_PHYLIP);
cout << myalign;
}
