X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracunweightedcommand.cpp;h=5fd26df8ccdd6e5510856ca26bd7574caa11ed43;hb=9b884118e97081d743c7b001216567f9b9131258;hp=77cd4d7d686ed5607c11eb07d2245c62f2ef2deb;hpb=438aa88dbc092d9c1c80ec3fa20c8e47f97101c4;p=mothur.git

diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index 77cd4d7..5fd26df 100644
--- a/unifracunweightedcommand.cpp
+++ b/unifracunweightedcommand.cpp
@@ -40,7 +40,7 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option)  {
 			//if the user changes the output directory command factory will send this info to us in the output parameter 
 			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	
 				outputDir = "";	
-				outputDir += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it	
+				outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it	
 			}
 							
 			//check for optional parameter and set defaults
@@ -48,7 +48,7 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option)  {
 			groups = validParameter.validFile(parameters, "groups", false);			
 			if (groups == "not found") { groups = ""; }
 			else { 
-				splitAtDash(groups, Groups);
+				m->splitAtDash(groups, Groups);
 				globaldata->Groups = Groups;
 			}
 				
@@ -56,26 +56,26 @@ UnifracUnweightedCommand::UnifracUnweightedCommand(string option)  {
 			convert(itersString, iters); 
 			
 			string temp = validParameter.validFile(parameters, "distance", false);			if (temp == "not found") { temp = "false"; }
-			phylip = isTrue(temp);
+			phylip = m->isTrue(temp);
 			
 			temp = validParameter.validFile(parameters, "random", false);					if (temp == "not found") { temp = "true"; }
-			random = isTrue(temp);
+			random = m->isTrue(temp);
 			
 			if (!random) {  iters = 0;  } //turn off random calcs
 			
 			//if user selects distance = true and no groups it won't calc the pairwise
 			if ((phylip) && (Groups.size() == 0)) {
 				groups = "all";
-				splitAtDash(groups, Groups);
+				m->splitAtDash(groups, Groups);
 				globaldata->Groups = Groups;
 			}
 		
 			if (abort == false) {
 				T = globaldata->gTree;
 				tmap = globaldata->gTreemap;
-				sumFile = outputDir + getSimpleName(globaldata->getTreeFile()) + ".uwsummary";
+				sumFile = outputDir + m->getSimpleName(globaldata->getTreeFile()) + ".uwsummary";
 				outputNames.push_back(sumFile);
-				openOutputFile(sumFile, outSum);
+				m->openOutputFile(sumFile, outSum);
 				
 				util = new SharedUtil();
 				util->setGroups(globaldata->Groups, tmap->namesOfGroups, allGroups, numGroups, "unweighted");	//sets the groups the user wants to analyze
@@ -125,6 +125,8 @@ int UnifracUnweightedCommand::execute() {
 		
 		if (abort == true) { return 0; }
 		
+		int start = time(NULL);
+		
 		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
@@ -143,8 +145,8 @@ int UnifracUnweightedCommand::execute() {
 			counter = 0;
 			
 			if (random)  {  
-				output = new ColumnFile(outputDir + getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".unweighted", itersString);
-				outputNames.push_back(outputDir + getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".unweighted");
+				output = new ColumnFile(outputDir + m->getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".unweighted", itersString);
+				outputNames.push_back(outputDir + m->getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".unweighted");
 			}
 			
 			
@@ -239,6 +241,8 @@ int UnifracUnweightedCommand::execute() {
 		
 		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  }	return 0; }
 		
+		m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run unifrac.unweighted."); m->mothurOutEndLine();
+		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 		for (int i = 0; i < outputNames.size(); i++) {	m->mothurOut(outputNames[i]); m->mothurOutEndLine();	}
@@ -317,11 +321,11 @@ void UnifracUnweightedCommand::printUWSummaryFile(int i) {
 /***********************************************************/
 void UnifracUnweightedCommand::createPhylipFile(int i) {
 	try {
-		string phylipFileName = outputDir + getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".unweighted.dist";
+		string phylipFileName = outputDir + m->getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".unweighted.dist";
 		outputNames.push_back(phylipFileName);
 		
 		ofstream out;
-		openOutputFile(phylipFileName, out);
+		m->openOutputFile(phylipFileName, out);
 			
 		//output numSeqs
 		out << globaldata->Groups.size() << endl;