//**********************************************************************************************************************
-ConcensusCommand::ConcensusCommand(string fileroot){
+ConcensusCommand::ConcensusCommand(string fileroot) {
try {
globaldata = GlobalData::getInstance();
abort = false;
}
catch(exception& e) {
- errorOut(e, "ConcensusCommand", "ConcensusCommand");
+ m->errorOut(e, "ConcensusCommand", "ConcensusCommand");
exit(1);
}
}
void ConcensusCommand::help(){
try {
- mothurOut("The consensus command can only be executed after a successful read.tree command.\n");
- mothurOut("The consensus command has no parameters.\n");
- mothurOut("The consensus command should be in the following format: consensus().\n");
- mothurOut("The consensus command output two files: .consensus.tre and .consensuspairs.\n");
- mothurOut("The .consensus.tre file contains the consensus tree of the trees in your input file.\n");
- mothurOut("The branch lengths are the percentage of trees in your input file that had the given pair.\n");
- mothurOut("The .consensuspairs file contains a list of the internal nodes in your tree. For each node, the pair that was used in the consensus tree \n");
- mothurOut("is reported with its percentage, as well as the other pairs that were seen for that node but not used and their percentages.\n\n");
+ m->mothurOut("The consensus command can only be executed after a successful read.tree command.\n");
+ m->mothurOut("The consensus command has no parameters.\n");
+ m->mothurOut("The consensus command should be in the following format: consensus().\n");
+ m->mothurOut("The consensus command output two files: .consensus.tre and .consensuspairs.\n");
+ m->mothurOut("The .consensus.tre file contains the consensus tree of the trees in your input file.\n");
+ m->mothurOut("The branch lengths are the percentage of trees in your input file that had the given pair.\n");
+ m->mothurOut("The .consensuspairs file contains a list of the internal nodes in your tree. For each node, the pair that was used in the consensus tree \n");
+ m->mothurOut("is reported with its percentage, as well as the other pairs that were seen for that node but not used and their percentages.\n\n");
}
catch(exception& e) {
- errorOut(e, "ConcensusCommand", "help");
+ m->errorOut(e, "ConcensusCommand", "help");
exit(1);
}
}
return 0;
}
catch(exception& e) {
- errorOut(e, "ConcensusCommand", "execute");
+ m->errorOut(e, "ConcensusCommand", "execute");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "ConcensusCommand", "buildConcensusTree");
+ m->errorOut(e, "ConcensusCommand", "buildConcensusTree");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "ConcensusCommand", "getSets");
+ m->errorOut(e, "ConcensusCommand", "getSets");
exit(1);
}
}
return smallest;
}
catch(exception& e) {
- errorOut(e, "ConcensusCommand", "getSmallest");
+ m->errorOut(e, "ConcensusCommand", "getSmallest");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "ConcensusCommand", "getNextAvailableSet");
+ m->errorOut(e, "ConcensusCommand", "getNextAvailableSet");
exit(1);
}
}
return rate;
}
catch(exception& e) {
- errorOut(e, "ConcensusCommand", "getSubgroupRating");
+ m->errorOut(e, "ConcensusCommand", "getSubgroupRating");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "ConcensusCommand", "getRestSet");
+ m->errorOut(e, "ConcensusCommand", "getRestSet");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "ConcensusCommand", "isSubset");
+ m->errorOut(e, "ConcensusCommand", "isSubset");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "ConcensusCommand", "findSpot");
+ m->errorOut(e, "ConcensusCommand", "findSpot");
exit(1);
}
}