moved utilities out of mothur.h and into mothurOut class.

[mothur.git] / unifracweightedcommand.cpp

diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index f092b0f2cf03c8e00d70e437af2219ad9c8def44..28d94d0adf502d21860099ba2928081169715e01 100644 (file)
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -40,7 +40,7 @@ UnifracWeightedCommand::UnifracWeightedCommand(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 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) {
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = ""; }
                        else { 
-                               splitAtDash(groups, Groups);
+                               m->splitAtDash(groups, Groups);
                                globaldata->Groups = Groups;
                        }
                                
@@ -56,10 +56,10 @@ UnifracWeightedCommand::UnifracWeightedCommand(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
 
@@ -67,8 +67,8 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) {
                        if (abort == false) {
                                T = globaldata->gTree;
                                tmap = globaldata->gTreemap;
-                               sumFile = outputDir + getSimpleName(globaldata->getTreeFile()) + ".wsummary";
-                               openOutputFile(sumFile, outSum);
+                               sumFile = outputDir + m->getSimpleName(globaldata->getTreeFile()) + ".wsummary";
+                               m->openOutputFile(sumFile, outSum);
                                outputNames.push_back(sumFile);
                                
                                util = new SharedUtil();
@@ -142,8 +142,8 @@ int UnifracWeightedCommand::execute() {
                        uScores.resize(numComp);  //data[0] = weightedscore AB, data[1] = weightedscore AC...
                        
                        if (random) {  
-                               output = new ColumnFile(outputDir + getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".weighted", itersString);  
-                               outputNames.push_back(outputDir + getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".weighted");
+                               output = new ColumnFile(outputDir + m->getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".weighted", itersString);  
+                               outputNames.push_back(outputDir + m->getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".weighted");
                        } 
 
                        userData = weighted->getValues(T[i]);  //userData[0] = weightedscore
@@ -348,10 +348,10 @@ void UnifracWeightedCommand::createPhylipFile() {
                //for each tree
                for (int i = 0; i < T.size(); i++) { 
                
-                       string phylipFileName = outputDir + getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".weighted.dist";
+                       string phylipFileName = outputDir + m->getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".weighted.dist";
                        outputNames.push_back(phylipFileName);
                        ofstream out;
-                       openOutputFile(phylipFileName, out);
+                       m->openOutputFile(phylipFileName, out);
                        
                        //output numSeqs
                        out << globaldata->Groups.size() << endl;