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

[mothur.git] / parsimonycommand.cpp

diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index b87e9c0b1ea0f5e84cbdf87a341c2fc6d393699d..3295de2d5c4db657b2a828c8be090476109d0f9a 100644 (file)
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -50,7 +50,7 @@ ParsimonyCommand::ParsimonyCommand(string option)  {
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = ""; globaldata->Groups.clear(); }
                        else { 
-                               splitAtDash(groups, Groups);
+                               m->splitAtDash(groups, Groups);
                                globaldata->Groups = Groups;
                        }
                                
@@ -64,20 +64,20 @@ ParsimonyCommand::ParsimonyCommand(string option)  {
                                        T = globaldata->gTree;
                                        tmap = globaldata->gTreemap;
                                        
-                                       if(outputDir == "") { outputDir += hasPath(globaldata->getTreeFile()); }
-                                       output = new ColumnFile(outputDir + getSimpleName(globaldata->getTreeFile())  +  ".parsimony", itersString);
-                                       outputNames.push_back(outputDir + getSimpleName(globaldata->getTreeFile())  +  ".parsimony");
+                                       if(outputDir == "") { outputDir += m->hasPath(globaldata->getTreeFile()); }
+                                       output = new ColumnFile(outputDir + m->getSimpleName(globaldata->getTreeFile())  +  ".parsimony", itersString);
+                                       outputNames.push_back(outputDir + m->getSimpleName(globaldata->getTreeFile())  +  ".parsimony");
                                        
-                                       sumFile = outputDir + getSimpleName(globaldata->getTreeFile()) + ".psummary";
-                                       openOutputFile(sumFile, outSum);
+                                       sumFile = outputDir + m->getSimpleName(globaldata->getTreeFile()) + ".psummary";
+                                       m->openOutputFile(sumFile, outSum);
                                        outputNames.push_back(sumFile);
                                }else { //user wants random distribution
                                        savetmap = globaldata->gTreemap;
                                        getUserInput();
                                        
-                                       if(outputDir == "") { outputDir += hasPath(randomtree); }
-                                       output = new ColumnFile(outputDir+ getSimpleName(randomtree), itersString);
-                                       outputNames.push_back(outputDir+ getSimpleName(randomtree));
+                                       if(outputDir == "") { outputDir += m->hasPath(randomtree); }
+                                       output = new ColumnFile(outputDir+ m->getSimpleName(randomtree), itersString);
+                                       outputNames.push_back(outputDir+ m->getSimpleName(randomtree));
                                }
                                
                                //set users groups to analyze