fixed unweighted calculator

[mothur.git] / unifracunweightedcommand.cpp

diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index bf2129c8b2bbc2e8e727c88bea45049464947bad..e2b085f76a8e951886d668915306667a7de1b5f2 100644 (file)
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -22,31 +22,7 @@ UnifracUnweightedCommand::UnifracUnweightedCommand() {
                openOutputFile(sumFile, outSum);
                distFile = globaldata->getTreeFile() + ".uwdistrib";
                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]);
-                       }
-               }
-               
+               setGroups(); //sets users groups to analyze
                convert(globaldata->getIters(), iters);  //how many random trees to generate
                unweighted = new Unweighted(tmap);
 
@@ -70,11 +46,18 @@ int UnifracUnweightedCommand::execute() {
                
                //format output
                outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint);
+               
+               outDist << "Groups Used ";
+               for (int m = 0; m < globaldata->Groups.size(); m++) {
+                       outDist << globaldata->Groups[m] << " ";
+               }
+               outDist << endl;
+               
                outDist << "Tree#" << '\t' << "Iter" << '\t' << "UWScore" << endl;
                
                //create new tree with same num nodes and leaves as users
                randT = new Tree();
-                       
+                               
                //get pscores for users trees
                for (int i = 0; i < T.size(); i++) {
                        cout << "Processing tree " << i+1 << endl;
@@ -183,6 +166,12 @@ void UnifracUnweightedCommand::printUnweightedFile() {
        try {
                //column headers
                
+               out << "Groups Used ";
+               for (int m = 0; m < globaldata->Groups.size(); m++) {
+                       out << globaldata->Groups[m] << " ";
+               }
+               out << endl;
+
                out << "Score" << '\t' << "UserFreq" << '\t' << "UserCumul" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
                                
                //format output
@@ -210,6 +199,13 @@ void UnifracUnweightedCommand::printUnweightedFile() {
 void UnifracUnweightedCommand::printUWSummaryFile() {
        try {
                //column headers
+               
+               outSum << "Groups Used ";
+               for (int m = 0; m < globaldata->Groups.size(); m++) {
+                       outSum << globaldata->Groups[m] << " ";
+               }
+               outSum << endl;
+
                outSum << "Tree#" << '\t'  <<  "UWScore" << '\t' << '\t' << "UWSig" <<  endl;
                
                //format output
@@ -255,4 +251,44 @@ void UnifracUnweightedCommand::saveRandomScores() {
        }
 }
 
-/***********************************************************/
\ No newline at end of file
+/***********************************************************/
+
+void UnifracUnweightedCommand::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 UnifracUnweightedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the UnifracUnweightedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }               
+
+}
+/*****************************************************************/
+