X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracunweightedcommand.cpp;h=65f30ebc949f4945023fd295224d00d52827d82b;hb=f18d75f9c996cb619a5051a7664620c0c5ae05fb;hp=3fa44b50014de39006037771bdc9899f0bc357f3;hpb=8f92612d5a69f5245e63a20657e7d93519c0769e;p=mothur.git

diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index 3fa44b5..65f30eb 100644
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -36,33 +36,36 @@ UnifracUnweightedCommand::UnifracUnweightedCommand() {
 /***********************************************************/
 int UnifracUnweightedCommand::execute() {
 	try {
-	
+
 		userData.resize(numComp,0);  //data[0] = unweightedscore 
 		randomData.resize(numComp,0); //data[0] = unweightedscore
 		//create new tree with same num nodes and leaves as users
-				
+		
+		outSum << "Tree#" << '\t' << "Groups" << '\t'  <<  "UWScore" <<'\t' << "UWSig" <<  endl;
+		cout << "Tree#" << '\t' << "Groups" << '\t'  <<  "UWScore" << '\t' << "UWSig" <<  endl;
+		
 		//get pscores for users trees
 		for (int i = 0; i < T.size(); i++) {
 			counter = 0;
 			unweightedFile = globaldata->getTreeFile()  + toString(i+1) + ".unweighted";
 			unweightedFileout = globaldata->getTreeFile() + "temp." + toString(i+1) + ".unweighted";
-						//column headers
-			outSum << "Tree# " << i+1 << endl;
-			outSum << "Comb" << '\t'  <<  "UWScore" << '\t' << '\t' << "UWSig" <<  endl;
-
+			
+			outSum << i+1 << '\t';
+			cout << i+1 << '\t';
+			
 			//get unweighted for users tree
 			rscoreFreq.resize(numComp);  
 			rCumul.resize(numComp);  
 			utreeScores.resize(numComp);  
 			UWScoreSig.resize(numComp); 
 
-			cout << "Processing tree " << i+1 << endl;
 			userData = unweighted->getValues(T[i]);  //userData[0] = unweightedscore
 			
 			//output scores for each combination
 			for(int k = 0; k < numComp; k++) {
 				//saves users score
 				utreeScores[k].push_back(userData[k]);
+
 			}
 			
 			//get unweighted scores for random trees
@@ -71,7 +74,6 @@ int UnifracUnweightedCommand::execute() {
 				randomData = unweighted->getValues(T[i], "", "");
 				
 				for(int k = 0; k < numComp; k++) {	
-//cout << "iter " << j << " comp " << k << " = " << randomData[k] << endl;
 					//add trees unweighted score to map of scores
 					it2 = rscoreFreq[k].find(randomData[k]);
 					if (it2 != rscoreFreq[k].end()) {//already have that score
@@ -83,6 +85,7 @@ int UnifracUnweightedCommand::execute() {
 					//add randoms score to validscores
 					validScores[randomData[k]] = randomData[k];
 				}
+				
 			}
 		
 		for(int a = 0; a < numComp; a++) {
@@ -99,6 +102,8 @@ int UnifracUnweightedCommand::execute() {
 			UWScoreSig[a].push_back(rCumul[a][userData[a]]);
 		}
 		
+		
+		
 		printUnweightedFile();
 		printUWSummaryFile();
 		
@@ -161,11 +166,17 @@ void UnifracUnweightedCommand::printUWSummaryFile() {
 				
 		//format output
 		outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
-		
+			
 		//print each line
+
 		for(int a = 0; a < numComp; a++) {
-			outSum << setprecision(6) << groupComb[a] << '\t' << '\t' << utreeScores[a][0] << '\t' << UWScoreSig[a][0] << endl;
-			cout << setprecision(6)  << groupComb[a] << '\t' << '\t' << utreeScores[a][0] << '\t' << UWScoreSig[a][0] << endl; 
+			if (UWScoreSig[a][0] > (1/(float)iters)) {
+				outSum << setprecision(6) << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << setprecision(globaldata->getIters().length()) << UWScoreSig[a][0] << endl;
+				cout << setprecision(6)  << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << setprecision(globaldata->getIters().length()) << UWScoreSig[a][0] << endl; 
+			}else {
+				outSum << setprecision(6) << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << setprecision(globaldata->getIters().length()) << "<" << (1/float(iters)) << endl;
+				cout << setprecision(6)  << groupComb[a]  << '\t' << utreeScores[a][0] << '\t' << setprecision(globaldata->getIters().length()) << "<" << (1/float(iters)) << endl; 
+			}
 		}
 		
 	}
@@ -202,26 +213,31 @@ void UnifracUnweightedCommand::setGroups() {
 					for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
 						globaldata->Groups.push_back(tmap->namesOfGroups[i]);
 						numGroups++;
-						allGroups += tmap->namesOfGroups[i];
+						allGroups += tmap->namesOfGroups[i] + "-";
 					}
+					allGroups = allGroups.substr(0, allGroups.length()-1);
 				}else {
 					for (int i = 0; i < globaldata->Groups.size(); i++) {
-						allGroups += globaldata->Groups[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++) {
 					globaldata->Groups.push_back(tmap->namesOfGroups[i]);
 					numGroups++;
-					allGroups += tmap->namesOfGroups[i];
+					allGroups += tmap->namesOfGroups[i] + "-";
 				}
+				allGroups = allGroups.substr(0, allGroups.length()-1);
 				globaldata->setGroups("");
 			}
 		}else {
 			for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
-				allGroups += tmap->namesOfGroups[i];
+				allGroups += tmap->namesOfGroups[i] + "-";
 			}
+			allGroups = allGroups.substr(0, allGroups.length()-1);
 			numGroups = 1;
 		}
 		
@@ -229,7 +245,7 @@ void UnifracUnweightedCommand::setGroups() {
 		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]);
+				groupComb.push_back(globaldata->Groups[r]+ "-" + globaldata->Groups[l]);
 				numComp++;
 			}
 		}
@@ -261,7 +277,7 @@ void UnifracUnweightedCommand::initFile(string label){
 			string inputBuffer;
 			getline(inFile, inputBuffer);
 		
-			out	<<  inputBuffer << '\t' << label + "Score" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;		
+			out	<<  inputBuffer << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;		
 		}else{
 			openOutputFile(unweightedFileout, out);
 			out	<< label + "Score" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
@@ -287,11 +303,12 @@ void UnifracUnweightedCommand::output(vector<double> data){
 		if(counter != 0){		
 			string inputBuffer;
 			getline(inFile, inputBuffer);
+//			out	<<  inputBuffer << setprecision(6) << '\t' << data[0] << setprecision(globaldata->getIters().length()) << '\t' << data[1] << '\t' << data[2] << endl;
 		
-			out	<<  inputBuffer << setprecision(6) << '\t' << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
+			out << inputBuffer << '\t' << setprecision(6) << data[0] << setprecision(globaldata->getIters().length())  << '\t' << data[1] << '\t' << data[2] << endl;
 		}
 		else{
-			out << setprecision(6) << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
+			out << setprecision(6) << data[0] << setprecision(globaldata->getIters().length())  << '\t' << data[1] << '\t' << data[2] << endl;
 		}
 
 	}