#include "consensuscommand.h"
+//**********************************************************************************************************************
+vector<string> ConcensusCommand::getValidParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ConcensusCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> ConcensusCommand::getRequiredParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ConcensusCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> ConcensusCommand::getRequiredFiles(){
+ try {
+ string AlignArray[] = {"tree","group"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ConcensusCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+ConcensusCommand::ConcensusCommand(){
+ try {
+ abort = true; calledHelp = true;
+ vector<string> tempOutNames;
+ outputTypes["tree"] = tempOutNames;
+ outputTypes["nodepairs"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ConcensusCommand", "ConcensusCommand");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
ConcensusCommand::ConcensusCommand(string fileroot) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["tree"] = tempOutNames;
+ outputTypes["nodepairs"] = tempOutNames;
filename = fileroot;
int ConcensusCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
else {
numNodes = t[0]->getNumNodes();
numLeaves = t[0]->getNumLeaves();
if (m->control_pressed) { return 0; }
//open file for pairing not included in the tree
- notIncluded = filename + ".cons.pairs";
- openOutputFile(notIncluded, out2);
+ notIncluded = filename + ".cons.pairs"; outputNames.push_back(notIncluded); outputTypes["nodepairs"].push_back(notIncluded);
+ m->openOutputFile(notIncluded, out2);
consensusTree = new Tree();
out2 << '\t' << it2->second << endl;
}
- outputFile = filename + ".cons.tre";
- openOutputFile(outputFile, out);
+ outputFile = filename + ".cons.tre"; outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
+ m->openOutputFile(outputFile, out);
- consensusTree->printForBoot(out);
+ consensusTree->print(out, "boot");
out.close(); out2.close();