X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=parsimonycommand.cpp;h=554d24bd93f76c94a223d33ce24159babd0f3e78;hb=d97b619c4297b1274c754d73a64792ba656b0a79;hp=989ea120447540884daac7f4f5e5496946b86d52;hpb=16bea3130e36addc54e2116dfbcd02d706ebee45;p=mothur.git

diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index 989ea12..554d24b 100644
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -27,7 +27,8 @@ ParsimonyCommand::ParsimonyCommand() {
 			openOutputFile(sumFile, outSum);
 			distFile = globaldata->getTreeFile() + ".pdistrib";
 			openOutputFile(distFile, outDist);
-
+			//set users groups to analyze
+			setGroups();
 		}else { //user wants random distribution
 			savetmap = globaldata->gTreemap;
 			getUserInput();
@@ -65,6 +66,7 @@ int ParsimonyCommand::execute() {
 			for (int i = 0; i < T.size(); i++) {
 				cout << "Processing tree " << i+1 << endl;
 				userData = pars->getValues(T[i]);  //userData[0] = pscore
+				cout << "Tree " << i+1 << " parsimony score = " << userData[0] << endl;
 				//update uscoreFreq
 				it = uscoreFreq.find(userData[0]);
 				if (it == uscoreFreq.end()) {//new score
@@ -164,6 +166,8 @@ int ParsimonyCommand::execute() {
 		
 		//reset randomTree parameter to ""
 		globaldata->setRandomTree("");
+		//reset groups parameter
+		globaldata->Groups.clear();
 		
 		return 0;
 		
@@ -286,3 +290,43 @@ void ParsimonyCommand::getUserInput() {
 }
 /***********************************************************/
 
+void ParsimonyCommand::setGroups() {
+	try {
+		//if the user has not entered specific groups to analyze then do them all
+		if (globaldata->Groups.size() != 0) {
+			//check that groups are valid
+			for (int i = 0; i < globaldata->Groups.size(); i++) {
+				if (tmap->isValidGroup(globaldata->Groups[i]) != true) {
+					cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
+					// erase the invalid group from globaldata->Groups
+					globaldata->Groups.erase (globaldata->Groups.begin()+i);
+				}
+			}
+			
+			//if the user only entered invalid groups
+			if (globaldata->Groups.size() == 0) { 
+				cout << "When using the groups parameter you must have at least 1 valid group. I will run the command using all the groups in your groupfile." << endl; 
+				for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
+					globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+				}
+			}
+					
+		}else {
+			for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
+				globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+			}
+		}
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the ParsimonyCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the ParsimonyCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}		
+
+}
+/*****************************************************************/
+
+