X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracweightedcommand.cpp;h=4ec2773d38eba93933015d8be8a77b8d078124bc;hb=3c5c4e255ee8c36feb9e97aebc4e792e6ff8c440;hp=fef08ff5268517744f2b185317352df28e607dd2;hpb=0190105145fbd3e02da8f23cb50841229e5d696f;p=mothur.git

diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index fef08ff..4ec2773 100644
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -20,49 +20,8 @@ UnifracWeightedCommand::UnifracWeightedCommand() {
 		openOutputFile(weightedFile, out);
 		sumFile = globaldata->getTreeFile() + ".wsummary";
 		openOutputFile(sumFile, outSum);
-		distFile = globaldata->getTreeFile() + ".wdistrib";
-		openOutputFile(distFile, outDist);
-		
-		//if the user has not entered specific groups to analyze then do them all
-		if (globaldata->Groups.size() == 0) {
-			numGroups = tmap->getNumGroups();
-		}else {
-			//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) { 
-				numGroups = tmap->getNumGroups();
-				cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl; 
-			}else if (globaldata->Groups.size() == 1) { 
-				cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
-				numGroups = tmap->getNumGroups();
-				globaldata->Groups.clear();
-			}else { numGroups = globaldata->Groups.size(); }
-		}
-		
-		//calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
-		numComp = 0;
-		int n = 1;
-		for (int i=1; i<numGroups; i++) { 
-			numComp += i; 
-			for (int l = n; l < numGroups; l++) {
-				//set group comparison labels
-				if (globaldata->Groups.size() != 0) {
-					groupComb.push_back(globaldata->Groups[i-1]+globaldata->Groups[l]);
-				}else {
-					groupComb.push_back(tmap->namesOfGroups[i-1]+tmap->namesOfGroups[l]);
-				}
-			}
-			n++;
-		}
-			
+				
+		setGroups();	//sets the groups the user wants to analyze			
 		convert(globaldata->getIters(), iters);  //how many random trees to generate
 		weighted = new Weighted(tmap);
 
@@ -88,11 +47,6 @@ int UnifracWeightedCommand::execute() {
 		totalrscoreFreq.resize(numComp); 
 		uCumul.resize(numComp); 	
 		
-		//format output
-		outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint);
-		outDist << "Tree#" << '\t' << "Iter" << '\t' << "Groups"<< '\t' << "WScore" << endl;
-
-		
 		//create new tree with same num nodes and leaves as users
 		randT = new Tree();
 		
@@ -141,9 +95,6 @@ int UnifracWeightedCommand::execute() {
 					
 					//add random score to valid scores
 					validScores[p][randomData[p]] = randomData[p];
-					
-					//output info to uwdistrib file
-					outDist << i+1 << '\t' << '\t'<< j+1 << '\t' << '\t' << groupComb[p] << '\t'<< randomData[p] << endl;
 				}
 			}
 			
@@ -198,9 +149,6 @@ int UnifracWeightedCommand::execute() {
 		printWeightedFile();
 		printWSummaryFile();
 		
-		//reset randomTree parameter to 0
-		globaldata->setRandomTree("0");
-		
 		//clear out users groups
 		globaldata->Groups.clear();
 		
@@ -255,6 +203,7 @@ void UnifracWeightedCommand::printWSummaryFile() {
 	try {
 		//column headers
 		outSum << "Tree#" << '\t' << "Groups" << '\t' << '\t' << "WScore" << '\t' << '\t' << "WSig" <<  endl;
+		cout << "Tree#" << '\t' << "Groups" << '\t' << '\t' << "WScore" << '\t' << '\t' << "WSig" <<  endl;
 		
 		//format output
 		outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
@@ -264,6 +213,7 @@ void UnifracWeightedCommand::printWSummaryFile() {
 		for (int i = 0; i < T.size(); i++) { 
 			for (int j = 0; j < numComp; j++) {
 				outSum << setprecision(6) << i+1 << '\t' << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << WScoreSig[count] << endl; 
+				cout << setprecision(6) << i+1 << '\t' << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << WScoreSig[count] << endl; 
 				count++;
 			}
 		}
@@ -307,3 +257,61 @@ void UnifracWeightedCommand::saveRandomScores() {
 }
 
 /***********************************************************/
+void UnifracWeightedCommand::setGroups() {
+	try {
+		//if the user has not entered specific groups to analyze then do them all
+		if (globaldata->Groups.size() == 0) {
+			numGroups = tmap->getNumGroups();
+		}else {
+			if (globaldata->getGroups() != "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) { 
+					numGroups = tmap->getNumGroups();
+					cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl; 
+				}else if (globaldata->Groups.size() == 1) { 
+					cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
+					numGroups = tmap->getNumGroups();
+					globaldata->Groups.clear();
+				}else { numGroups = globaldata->Groups.size(); }
+			}else { //users wants all groups
+				numGroups = tmap->getNumGroups();
+				globaldata->Groups.clear();
+				globaldata->setGroups("");
+			}
+		}
+		
+		//calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
+		numComp = 0;
+		int n = 1;
+		for (int i=1; i<numGroups; i++) { 
+			numComp += i; 
+			for (int l = n; l < numGroups; l++) {
+				//set group comparison labels
+				if (globaldata->Groups.size() != 0) {
+					groupComb.push_back(globaldata->Groups[i-1]+globaldata->Groups[l]);
+				}else {
+					groupComb.push_back(tmap->namesOfGroups[i-1]+tmap->namesOfGroups[l]);
+				}
+			}
+			n++;
+		}
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the UnifracWeightedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+}
+