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

[mothur.git] / otuhierarchycommand.cpp

diff --git a/otuhierarchycommand.cpp b/otuhierarchycommand.cpp
index 05d6443725be6028411573b6ee280220cb52ff0c..2c71cd56aa8a6341def135ec0a7ddcb092993885 100644 (file)
--- a/otuhierarchycommand.cpp
+++ b/otuhierarchycommand.cpp
@@ -41,7 +41,7 @@ OtuHierarchyCommand::OtuHierarchyCommand(string option) {
                                it = parameters.find("list");
                                //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["list"] = inputDir + it->second;             }
                                }
@@ -54,7 +54,7 @@ OtuHierarchyCommand::OtuHierarchyCommand(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(listFile); //if user entered a file with a path then preserve it   
+                               outputDir += m->hasPath(listFile); //if user entered a file with a path then preserve it        
                        }
                        
                        //check for optional parameter and set defaults
@@ -62,7 +62,7 @@ OtuHierarchyCommand::OtuHierarchyCommand(string option) {
                        label = validParameter.validFile(parameters, "label", false);                   
                        if (label == "not found") { m->mothurOut("label is a required parameter for the otu.hierarchy command."); m->mothurOutEndLine(); abort = true; }
                        else { 
-                               splitAtDash(label, labels);
+                               m->splitAtDash(label, labels);
                                if (labels.size() != 2) { m->mothurOut("You must provide 2 labels."); m->mothurOutEndLine(); abort = true; }
                        }       
                        
@@ -142,8 +142,8 @@ int OtuHierarchyCommand::execute(){
                }
                
                ofstream out;
-               string outputFileName = outputDir + getRootName(getSimpleName(listFile)) + lists[0].getLabel() + "-" + lists[1].getLabel() + ".otu.hierarchy";
-               openOutputFile(outputFileName, out);
+               string outputFileName = outputDir + m->getRootName(m->getSimpleName(listFile)) + lists[0].getLabel() + "-" + lists[1].getLabel() + ".otu.hierarchy";
+               m->openOutputFile(outputFileName, out);
                
                //go through each bin in "big" otu and output the bins in "little" otu which created it
                for (int i = 0; i < lists[1].getNumBins(); i++) {
@@ -211,7 +211,7 @@ vector<ListVector> OtuHierarchyCommand::getListVectors() {
 
                //open file
                ifstream in;
-               openInputFile(listFile, in);
+               m->openInputFile(listFile, in);
                
                //get first list vector in file
                ListVector* list = NULL;
@@ -220,7 +220,7 @@ vector<ListVector> OtuHierarchyCommand::getListVectors() {
                        pos = in.tellg();
                        lastPos = pos;
                        list = new ListVector(in);  
-                       gobble(in);
+                       m->gobble(in);
                        lastLabel = list->getLabel();
                }
                
@@ -240,7 +240,7 @@ vector<ListVector> OtuHierarchyCommand::getListVectors() {
                        }
                
                        //you have a label the user want that is smaller than this label and the last label has not already been processed 
-                       if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+                       if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
                                string saveLabel = list->getLabel();
                                int savePos = in.tellg();
                                
@@ -271,7 +271,7 @@ vector<ListVector> OtuHierarchyCommand::getListVectors() {
                        if (!in.eof())  {       
                                pos = in.tellg();
                                list = new ListVector(in);  
-                               gobble(in);
+                               m->gobble(in);
                        }else { list = NULL; }
                }