started shared utilities, updates to venn and heatmap added tree.groups command

[mothur.git] / parsimonycommand.cpp

diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index 86f8d013c59449b96009ba07859be7e0985cc141..4fa4ec5ed0943614bf4da9d5a1f03b5d8f706a42 100644 (file)
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -33,7 +33,17 @@ ParsimonyCommand::ParsimonyCommand() {
                }
                
                //set users groups to analyze
-               setGroups();
+               util = new SharedUtil();
+               util->setGroups(globaldata->Groups, tmap->namesOfGroups, allGroups, numGroups, "unweighted");   //sets the groups the user wants to analyze
+               util->getCombos(groupComb, globaldata->Groups, numComp);
+               globaldata->setGroups("");
+               
+               //ABC
+               if (numComp != 1) {
+                       groupComb.push_back(allGroups);
+                       numComp++;
+               }
+
                convert(globaldata->getIters(), iters);  //how many random trees to generate
                pars = new Parsimony(tmap);
                counter = 0;
@@ -194,7 +204,7 @@ int ParsimonyCommand::execute() {
                //reset randomTree parameter to ""
                globaldata->setRandomTree("");
                //reset groups parameter
-               globaldata->Groups.clear();  globaldata->setGroups("");
+               globaldata->Groups.clear(); 
                
                return 0;
                
@@ -330,90 +340,6 @@ void ParsimonyCommand::getUserInput() {
                exit(1);
        }
 }
-/***********************************************************/
-
-void ParsimonyCommand::setGroups() {
-       try {
-               string allGroups = "";
-               numGroups = 0;
-               //if the user has not entered specific groups to analyze then do them all
-               if (globaldata->Groups.size() != 0) {
-                       if (globaldata->Groups[0] != "all") {
-                               //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++) {
-                                               if (tmap->namesOfGroups[i] != "xxx") {
-                                                       allGroups += tmap->namesOfGroups[i] + "-";
-                                                       globaldata->Groups.push_back(tmap->namesOfGroups[i]);
-                                                       numGroups++;
-                                               }
-                                       }
-                                       allGroups = allGroups.substr(0, allGroups.length()-1);
-                               }else {
-                                       for (int i = 0; i < globaldata->Groups.size(); i++) {
-                                               allGroups += globaldata->Groups[i] + "-";
-                                               numGroups++;
-                                       }
-                                       allGroups = allGroups.substr(0, allGroups.length()-1);
-                               }
-                       }else{//user has enter "all" and wants the default groups
-                               globaldata->Groups.clear();
-                               for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
-                                       if (tmap->namesOfGroups[i] != "xxx") {
-                                               globaldata->Groups.push_back(tmap->namesOfGroups[i]);
-                                               numGroups++;
-                                               allGroups += tmap->namesOfGroups[i] + "-";
-                                       }
-                               }
-                               allGroups = allGroups.substr(0, allGroups.length()-1);
-                               globaldata->setGroups("");
-                       }
-               }else {
-                       for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
-                               if (tmap->namesOfGroups[i] != "xxx") {
-                                       allGroups += tmap->namesOfGroups[i] + "-";
-                               }
-                       }
-                       allGroups = allGroups.substr(0, allGroups.length()-1);
-                       numGroups = 1;
-               }
-               
-               //calculate number of comparsions
-               numComp = 0;
-               for (int r=0; r<numGroups; r++) { 
-                       for (int l = r+1; l < numGroups; l++) {
-                               groupComb.push_back(globaldata->Groups[r]+ "-" +globaldata->Groups[l]);
-                               numComp++;
-                       }
-               }
-               
-               //ABC
-               if (numComp != 1) {
-                       groupComb.push_back(allGroups);
-                       numComp++;
-               }
-               
-       }
-       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);
-       }               
-
-}
 /*****************************************************************/
 
 void ParsimonyCommand::initFile(string label){