sped up unifrac weighted.

[mothur.git] / unifracunweightedcommand.cpp

diff --git a/unifracunweightedcommand.cpp b/unifracunweightedcommand.cpp
index 77cd4d7d686ed5607c11eb07d2245c62f2ef2deb..5fd26df8ccdd6e5510856ca26bd7574caa11ed43 100644 (file)
--- 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;