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

[mothur.git] / treegroupscommand.cpp

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index c4e58c28b3a7c56892981c7e221b738daa610ccd..eb3c33481d4ef68199f2b42e452ea93c1679bbf4 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -58,7 +58,7 @@ TreeGroupCommand::TreeGroupCommand(string option)  {
                                it = parameters.find("phylip");
                                //user has given a template file
                                if(it != parameters.end()){ 
-                                       path = hasPath(it->second);
+                                       path = m->hasPath(it->second);
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["phylip"] = inputDir + it->second;           }
                                }
@@ -66,7 +66,7 @@ TreeGroupCommand::TreeGroupCommand(string option)  {
                                it = parameters.find("column");
                                //user has given a template file
                                if(it != parameters.end()){ 
-                                       path = hasPath(it->second);
+                                       path = m->hasPath(it->second);
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["column"] = inputDir + it->second;           }
                                }
@@ -74,7 +74,7 @@ TreeGroupCommand::TreeGroupCommand(string option)  {
                                it = parameters.find("name");
                                //user has given a template file
                                if(it != parameters.end()){ 
-                                       path = hasPath(it->second);
+                                       path = m->hasPath(it->second);
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["name"] = inputDir + it->second;             }
                                }
@@ -111,7 +111,7 @@ TreeGroupCommand::TreeGroupCommand(string option)  {
                        label = validParameter.validFile(parameters, "label", false);                   
                        if (label == "not found") { label = ""; }
                        else { 
-                               if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
+                               if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
                                else { allLines = 1;  }
                        }
                        
@@ -124,7 +124,7 @@ TreeGroupCommand::TreeGroupCommand(string option)  {
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = ""; }
                        else { 
-                               splitAtDash(groups, Groups);
+                               m->splitAtDash(groups, Groups);
                                globaldata->Groups = Groups;
                        }
                                
@@ -133,7 +133,7 @@ TreeGroupCommand::TreeGroupCommand(string option)  {
                        else { 
                                 if (calc == "default")  {  calc = "jclass-thetayc";  }
                        }
-                       splitAtDash(calc, Estimators);
+                       m->splitAtDash(calc, Estimators);
 
                        string temp;
                        temp = validParameter.validFile(parameters, "precision", false);                        if (temp == "not found") { temp = "100"; }
@@ -146,7 +146,7 @@ TreeGroupCommand::TreeGroupCommand(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       
                        }
 
                                
@@ -322,7 +322,7 @@ int TreeGroupCommand::execute(){
                        if (m->control_pressed) { return 0; }
 
                        //create a new filename
-                       outputFile = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "tre"; 
+                       outputFile = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "tre";   
                        outputNames.push_back(outputFile);
                                
                        createTree();
@@ -512,7 +512,7 @@ int TreeGroupCommand::makeSimsShared() {
                                userLabels.erase(lookup[0]->getLabel());
                        }
                        
-                       if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+                       if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
                                string saveLabel = lookup[0]->getLabel();
                        
                                for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
@@ -593,7 +593,7 @@ int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
                                        for (int g = 0; g < numGroups; g++) {   index[g] = g;   }
                
                                        //create a new filename
-                                       outputFile = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".tre";                              
+                                       outputFile = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".tre";                                
                                        outputNames.push_back(outputFile);
                                                                                                
                                        for (int k = 0; k < thisLookup.size(); k++) {