parsimony command now uses groups, fixed bug with unweighted groups

[mothur.git] / unifracunweightedcommand.cpp

diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index 8adff2d896f811d46e80b806acf45261d759c69b..bf2129c8b2bbc2e8e727c88bea45049464947bad 100644 (file)
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -23,6 +23,30 @@ UnifracUnweightedCommand::UnifracUnweightedCommand() {
                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]);
+                       }
+               }
+               
                convert(globaldata->getIters(), iters);  //how many random trees to generate
                unweighted = new Unweighted(tmap);
 
@@ -93,49 +117,52 @@ int UnifracUnweightedCommand::execute() {
                                outDist << i+1 << '\t' << '\t'<< j+1 << '\t' << '\t' << randomData[0] << endl;
                        }
                        
+                       saveRandomScores(); //save all random scores for unweighted file
+                       
                        //find the signifigance of the score
-                       float rcumul = 0.0000;
+                       float rcumul = 1.0000;
                        for (it = rscoreFreq.begin(); it != rscoreFreq.end(); it++) { 
+                               rCumul[it->first] = rcumul;
                                //get percentage of random trees with that info
                                rscoreFreq[it->first] /= iters; 
-                               rcumul+= it->second;  
-                               rCumul[it->first] = rcumul;
+                               rcumul-= it->second;  
+                               
                        }
                        
                        //save the signifigance of the users score for printing later
                        UWScoreSig.push_back(rCumul[userData[0]]);
                        
-                       saveRandomScores(); //save all random scores for unweighted file
-               
+                       
                        //clear random data
                        rscoreFreq.clear();  //you clear this because in the summary file you want the unweighted signifinance to be relative to these 1000 trees.
                        rCumul.clear();
                }
                
-               float ucumul = 0.0000;
-               float rcumul = 0.0000;
+               float ucumul = 1.0000;
+               float rcumul = 1.0000;
                //this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
                for (it = validScores.begin(); it != validScores.end(); it++) { 
                        it2 = uscoreFreq.find(it->first);
-                       //user data has that score 
-                       if (it2 != uscoreFreq.end()) { uscoreFreq[it->first] /= T.size(); ucumul+= it2->second;  }
-                       else { uscoreFreq[it->first] = 0.0000; } //no user trees with that score
                        //make uCumul map
                        uCumul[it->first] = ucumul;
-                       
+                       //user data has that score 
+                       if (it2 != uscoreFreq.end()) { uscoreFreq[it->first] /= T.size(); ucumul-= it2->second;  }
+                       else { uscoreFreq[it->first] = 0.0000; } //no user trees with that score
+                                               
                        //make rscoreFreq map and rCumul
                        it2 = totalrscoreFreq.find(it->first);
+                       rCumul[it->first] = rcumul;
                        //get percentage of random trees with that info
-                       if (it2 != totalrscoreFreq.end()) {  totalrscoreFreq[it->first] /= (iters*T.size()); rcumul+= it2->second;  }
+                       if (it2 != totalrscoreFreq.end()) {  totalrscoreFreq[it->first] /= (iters*T.size()); rcumul-= it2->second;  }
                        else { totalrscoreFreq[it->first] = 0.0000; } //no random trees with that score
-                       rCumul[it->first] = rcumul;
+                       
                }
                
                printUnweightedFile();
                printUWSummaryFile();
                
-               //reset randomTree parameter to 0
-               globaldata->setRandomTree("0");
+               //reset groups parameter
+               globaldata->Groups.clear();
                
                delete randT;
                
@@ -207,15 +234,14 @@ void UnifracUnweightedCommand::printUWSummaryFile() {
 /***********************************************************/
 void UnifracUnweightedCommand::saveRandomScores() {
        try {
-               //update total map with new random scores
                for (it = rscoreFreq.begin(); it != rscoreFreq.end(); it++) { 
                        //does this score already exist in the total map
                        it2 = totalrscoreFreq.find(it->first);
                        //if yes then add them
                        if (it2 != totalrscoreFreq.end()) { 
-                               it2->second += it->second;
+                               totalrscoreFreq[it->first] += rscoreFreq[it->first];
                        }else{ //its a new score
-                               totalrscoreFreq[it->first] = 1;
+                               totalrscoreFreq[it->first] = rscoreFreq[it->first];
                        }
                }
        }