#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();
delete consensusTree;
+ //set first tree file as new current treefile
+ string currentTree = "";
+ itTypes = outputTypes.find("tree");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { currentTree = (itTypes->second)[0]; m->setTreeFile(currentTree); }
+ }
+
return 0;
}
catch(exception& e) {
while (nodePairsCopy.size() != 0) {
if (m->control_pressed) { return 1; }
- vector<string> small = getSmallest(nodePairsCopy);
+ vector<string> smallOne = getSmallest(nodePairsCopy);
- int subgrouprate = getSubgroupRating(small);
+ int subgrouprate = getSubgroupRating(smallOne);
- nodePairsInitialRate[small] = nodePairs[small] + subgrouprate;
+ nodePairsInitialRate[smallOne] = nodePairs[smallOne] + subgrouprate;
- nodePairsCopy.erase(small);
+ nodePairsCopy.erase(smallOne);
}
return 0;