fixed unweighted calculator

[mothur.git] / parsimonycommand.cpp

diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index fe5a1dd251899818715cb52c14ac7c73a40630b2..554d24bd93f76c94a223d33ce24159babd0f3e78 100644 (file)
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -27,31 +27,8 @@ ParsimonyCommand::ParsimonyCommand() {
                        openOutputFile(sumFile, outSum);
                        distFile = globaldata->getTreeFile() + ".pdistrib";
                        openOutputFile(distFile, outDist);
-                       
-                       //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]);
-                               }
-                       }
-
+                       //set users groups to analyze
+                       setGroups();
                }else { //user wants random distribution
                        savetmap = globaldata->gTreemap;
                        getUserInput();
@@ -313,3 +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);
+       }               
+
+}
+/*****************************************************************/
+
+