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; }