changed unifrac.weighted()

[mothur.git] / parsimonycommand.cpp

diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index 59dca88751edfb115cc3c83fcc5c85935b52b9d3..1a493bd86df990266d4504a5e938a7e78e721f44 100644 (file)
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -25,8 +25,6 @@ ParsimonyCommand::ParsimonyCommand() {
                        openOutputFile(parsFile, out);
                        sumFile = globaldata->getTreeFile() + ".psummary";
                        openOutputFile(sumFile, outSum);
-                       distFile = globaldata->getTreeFile() + ".pdistrib";
-                       openOutputFile(distFile, outDist);
                        //set users groups to analyze
                        setGroups();
                }else { //user wants random distribution
@@ -57,10 +55,6 @@ int ParsimonyCommand::execute() {
                userData.resize(1,0);  //data[0] = pscore.
                randomData.resize(1,0);  //data[0] = pscore.
                
-               //format output
-               outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint);
-               outDist << "RandomTree#" << '\t' << "ParsScore" << endl;
-               
                if (randomtree == "") {
                        copyUserTree = new Tree();
                        //get pscores for users trees
@@ -104,9 +98,6 @@ int ParsimonyCommand::execute() {
                                //add randoms score to validscores
                                validScores[randomData[0]] = randomData[0];
                                
-                               //output info to pdistrib file
-                               outDist << j+1 << '\t'<< '\t' << randomData[0] << endl;
-                                       
                                delete randT;
                        }
                }else {
@@ -170,7 +161,7 @@ int ParsimonyCommand::execute() {
                //reset randomTree parameter to ""
                globaldata->setRandomTree("");
                //reset groups parameter
-               globaldata->Groups.clear();
+               globaldata->Groups.clear();  globaldata->setGroups("");
                
                return 0;
                
@@ -297,23 +288,29 @@ 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 (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; 
+                               //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{//user has enter "all" and wants the default groups
                                for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
                                        globaldata->Groups.push_back(tmap->namesOfGroups[i]);
                                }
+                               globaldata->setGroups("");
                        }
-                                       
                }else {
                        for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
                                globaldata->Groups.push_back(tmap->namesOfGroups[i]);