X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracunweightedcommand.cpp;h=bf2129c8b2bbc2e8e727c88bea45049464947bad;hb=692e0c1f69a78b568dc85cbdcea9fb6c189e2e6c;hp=8adff2d896f811d46e80b806acf45261d759c69b;hpb=d037597badc8d18e235c59f0c1114180edb7f98f;p=mothur.git

diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index 8adff2d..bf2129c 100644
--- 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];
 			}
 		}
 	}