From: pschloss <pschloss>
Date: Sat, 7 Mar 2009 18:02:15 +0000 (+0000)
Subject: mucked around some with the output in the unifrac.weighted, unifrac.unweighted, and... 
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=a85da7303079652b569291eacb9c2964060e072b

mucked around some with the output in the unifrac.weighted, unifrac.unweighted, and parsimony commands
---

diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index 4b3435e..f718653 100644
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -226,8 +226,8 @@ void ParsimonyCommand::printParsimonyFile() {
 void ParsimonyCommand::printUSummaryFile() {
 	try {
 		//column headers
-		outSum << "Tree#" << '\t' << "Comb" << '\t'  <<  "ParsScore" << '\t' << '\t' << "ParsSig" <<  endl;
-		cout << "Tree#" << '\t' << "Comb" << '\t'  <<  "ParsScore" << '\t' << '\t' << "ParsSig" <<  endl;
+		outSum << "Tree#" << '\t' << "Groups" << '\t'  <<  "ParsScore" << '\t' << "ParsSig" <<  endl;
+		cout << "Tree#" << '\t' << "Groups" << '\t'  <<  "ParsScore" << '\t' << "ParsSig" <<  endl;
 		
 		//format output
 		outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
@@ -237,11 +237,11 @@ void ParsimonyCommand::printUSummaryFile() {
 		for (int i = 0; i< T.size(); i++) {
 			for(int a = 0; a < numComp; a++) {
 				if (UScoreSig[a][i] > (1/(float)iters)) {
-					outSum << setprecision(globaldata->getIters().length()) << i+1 << '\t' << groupComb[a] << '\t' << '\t' << userTreeScores[a][i] << '\t' << UScoreSig[a][i] << endl;
-					cout << setprecision(globaldata->getIters().length()) << i+1 << '\t' << groupComb[a] << '\t' << '\t' << userTreeScores[a][i] << '\t' << UScoreSig[a][i] << endl;
+					outSum << setprecision(globaldata->getIters().length()) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << '\t' << UScoreSig[a][i] << endl;
+					cout << setprecision(globaldata->getIters().length()) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << '\t' << UScoreSig[a][i] << endl;
 				}else {
-					outSum << setprecision(globaldata->getIters().length()) << i+1 << '\t' << groupComb[a] << '\t' << '\t' << userTreeScores[a][i] << '\t' << "<" << (1/float(iters)) << endl;
-					cout << setprecision(globaldata->getIters().length()) << i+1 << '\t' << groupComb[a] << '\t' << '\t' << userTreeScores[a][i] << '\t' << "<" << (1/float(iters)) << endl;
+					outSum << setprecision(globaldata->getIters().length()) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << '\t' << "<" << (1/float(iters)) << endl;
+					cout << setprecision(globaldata->getIters().length()) << i+1 << '\t' << groupComb[a] << '\t' << userTreeScores[a][i] << '\t' << "<" << (1/float(iters)) << endl;
 				}
 			}
 		}
@@ -397,7 +397,7 @@ void ParsimonyCommand::initFile(string label){
 			if (randomtree == "") {
 				out <<  inputBuffer << '\t' << label + "Score" << '\t' << label + "UserFreq" << '\t' << label + "UserCumul" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
 			}else {
-				out <<  inputBuffer << '\t' << label + "Score" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
+				out <<  inputBuffer << '\t' << "Score" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
 			}
 		}else{
 			openOutputFile(parsFileout, out);
@@ -405,7 +405,7 @@ void ParsimonyCommand::initFile(string label){
 			if (randomtree == "") {
 				out << label + "Score" << '\t' << label + "UserFreq" << '\t' << label + "UserCumul" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
 			}else {
-				out << label + "Score" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
+				out << "Score" << '\t' << "RandFreq" << '\t' << "RandCumul" << endl;
 			}
 		}
 
diff --git a/readtreecommand.cpp b/readtreecommand.cpp
index 68f1f92..63c6226 100644
--- a/readtreecommand.cpp
+++ b/readtreecommand.cpp
@@ -52,7 +52,6 @@ int ReadTreeCommand::execute(){
 		for (int i = 0; i < T.size(); i++) {
 			T[i]->assembleTree();
 		}
-T[0]->createNewickFile("treeout");		
 		return 0;
 	}
 	catch(exception& e) {
diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index 6e217c8..6fd986f 100644
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -48,10 +48,10 @@ int UnifracUnweightedCommand::execute() {
 			unweightedFileout = globaldata->getTreeFile() + "temp." + toString(i+1) + ".unweighted";
 			
 			//column headers
-			outSum << "Tree# " << i+1 << endl;
-			outSum << "Comb" << '\t'  <<  "UWScore" << '\t' << '\t' << "UWSig" <<  endl;
-			cout << "Tree# " << i+1 << endl;
-			cout << "Comb" << '\t'  <<  "UWScore" << '\t' << '\t' << "UWSig" <<  endl;
+//			outSum << "Tree# " << i+1 << endl;
+			outSum << "Tree#" << '\t' << "Groups" << '\t'  <<  "UWScore" <<'\t' << "UWSig" <<  endl;
+//			cout << "Tree# " << i+1 << endl;
+			cout << "Tree#" << '\t' << "Groups" << '\t'  <<  "UWScore" << '\t' << "UWSig" <<  endl;
 
 
 			//get unweighted for users tree
@@ -163,15 +163,17 @@ 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++) {
-			if (UWScoreSig[a][0] > (1/(float)iters)) {
-				outSum << setprecision(globaldata->getIters().length()) << groupComb[a] << '\t' << '\t' << utreeScores[a][0] << '\t' << UWScoreSig[a][0] << endl;
-				cout << setprecision(globaldata->getIters().length())  << groupComb[a] << '\t' << '\t' << utreeScores[a][0] << '\t' << UWScoreSig[a][0] << endl; 
-			}else {
-				outSum << setprecision(globaldata->getIters().length()) << groupComb[a] << '\t' << '\t' << utreeScores[a][0] << '\t' << "<" << (1/float(iters)) << endl;
-				cout << setprecision(globaldata->getIters().length())  << groupComb[a] << '\t' << '\t' << utreeScores[a][0] << '\t' << "<" << (1/float(iters)) << endl; 
+		for (int i = 0; i< T.size(); i++) {
+			for(int a = 0; a < numComp; a++) {
+				if (UWScoreSig[a][i] > (1/(float)iters)) {
+					outSum << setprecision(globaldata->getIters().length()) << i+1 << '\t' << groupComb[a] << '\t' << utreeScores[a][i] << '\t' << UWScoreSig[a][i] << endl;
+					cout << setprecision(globaldata->getIters().length()) << i+1 << '\t' << groupComb[a] << '\t' << utreeScores[a][i] << '\t' << UWScoreSig[a][i] << endl;
+				}else {
+					outSum << setprecision(globaldata->getIters().length()) << i+1 << '\t' << groupComb[a] << '\t' << utreeScores[a][i] << '\t' << "<" << (1/float(iters)) << endl;
+					cout << setprecision(globaldata->getIters().length()) << i+1 << '\t' << groupComb[a] << '\t' << utreeScores[a][i] << '\t' << "<" << (1/float(iters)) << endl;
+				}
 			}
 		}
 		
@@ -273,7 +275,7 @@ 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;
@@ -299,11 +301,12 @@ 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(globaldata->getIters().length()) << '\t' << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
+			out	<<  inputBuffer << setprecision(globaldata->getIters().length()-1) << '\t' << data[1] << '\t' << data[2] << endl;
 		}
 		else{
-			out << setprecision(globaldata->getIters().length()) << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
+			out << setprecision(6) << data[0] << setprecision(globaldata->getIters().length()-1) << '\t' << data[1] << '\t' << data[2] << endl;
 		}
 
 	}
diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index 6d8f75b..49f6631 100644
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -164,8 +164,8 @@ void UnifracWeightedCommand::printWeightedFile() {
 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;
+		outSum << "Tree#" << '\t' << "Groups" << '\t' << "WScore" << '\t' << "WSig" <<  endl;
+		cout << "Tree#" << '\t' << "Groups" << '\t' << "WScore" << '\t' << "WSig" <<  endl;
 		
 		//format output
 		outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);
@@ -175,11 +175,11 @@ void UnifracWeightedCommand::printWSummaryFile() {
 		for (int i = 0; i < T.size(); i++) { 
 			for (int j = 0; j < numComp; j++) {
 				if (WScoreSig[count] > (1/(float)iters)) {
-					outSum << setprecision(globaldata->getIters().length()) << i+1 << '\t' << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << WScoreSig[count] << endl; 
-					cout << setprecision(globaldata->getIters().length()) << i+1 << '\t' << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << WScoreSig[count] << endl; 
+					outSum << setprecision(globaldata->getIters().length()) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << WScoreSig[count] << endl; 
+					cout << setprecision(globaldata->getIters().length()) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << WScoreSig[count] << endl; 
 				}else{
-					outSum << setprecision(globaldata->getIters().length()) << i+1 << '\t' << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << "<" << (1/float(iters)) << endl; 
-					cout << setprecision(globaldata->getIters().length()) << i+1 << '\t' << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << "<" << (1/float(iters)) << endl; 
+					outSum << setprecision(globaldata->getIters().length()) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << "<" << (1/float(iters)) << endl; 
+					cout << setprecision(globaldata->getIters().length()) << i+1 << '\t' << groupComb[j] << '\t' << utreeScores[count] << '\t' << "<" << (1/float(iters)) << endl; 
 				}
 				count++;
 			}
@@ -340,7 +340,7 @@ void UnifracWeightedCommand::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(weightedFileout, out);
 			out	<< label + "Score" << '\t' << label + "RandFreq" << '\t' << label + "RandCumul" << endl;
@@ -366,13 +366,13 @@ void UnifracWeightedCommand::output(vector<double> data){
 		if(counter != 0){		
 			string inputBuffer;
 			getline(inFile, inputBuffer);
-		
-			out	<<  inputBuffer << setprecision(globaldata->getIters().length()) << '\t' << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
+			
+			out	<<  inputBuffer << setprecision(globaldata->getIters().length()-1) << '\t' << data[1] << '\t' << data[2] << endl;
 		}
 		else{
-			out << setprecision(globaldata->getIters().length()) << data[0] << '\t' << data[1] << '\t' << data[2] << endl;
+			out << setprecision(6) << data[0] << setprecision(globaldata->getIters().length()-1) << '\t' << data[1] << '\t' << data[2] << endl;
 		}
-
+		
 	}
 	catch(exception& e) {
 		cout << "Standard Error: " << e.what() << " has occurred in the UnifracWeightedCommand class Function output. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";