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

[mothur.git] / parselistscommand.cpp

diff --git a/parselistscommand.cpp b/parselistscommand.cpp
index d09910b48de9003865f06fd21d165a71e989dde9..4b24236e3497ab67f2be5299163798a9f43e8667 100644 (file)
--- a/parselistscommand.cpp
+++ b/parselistscommand.cpp
@@ -42,7 +42,7 @@ ParseListCommand::ParseListCommand(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;             }
                                }
@@ -50,7 +50,7 @@ ParseListCommand::ParseListCommand(string option)  {
                                it = parameters.find("group");
                                //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["group"] = inputDir + it->second;            }
                                }
@@ -83,7 +83,7 @@ ParseListCommand::ParseListCommand(string option)  {
                        label = validParameter.validFile(parameters, "label", false);                   
                        if (label == "not found") { label = "";  allLines = 1; }
                        else { 
-                               if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
+                               if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
                                else { allLines = 1;  }
                        }
                }
@@ -120,7 +120,7 @@ int ParseListCommand::execute(){
                if (abort == true) {    return 0;       }
                
                //set fileroot
-               string fileroot = outputDir + getRootName(getSimpleName(listfile));
+               string fileroot = outputDir + m->getRootName(m->getSimpleName(listfile));
                vector<string> outputNames;
                
                //fill filehandles with neccessary ofstreams
@@ -132,7 +132,7 @@ int ParseListCommand::execute(){
                        
                        string filename = fileroot +  groupMap->namesOfGroups[i] + ".list";
                        outputNames.push_back(filename);
-                       openOutputFile(filename, *temp);
+                       m->openOutputFile(filename, *temp);
                }
                
                //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
@@ -168,7 +168,7 @@ int ParseListCommand::execute(){
                                        userLabels.erase(list->getLabel());
                        }
                        
-                       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();
                                        
                                        delete list;
@@ -278,7 +278,7 @@ int ParseListCommand::parse(ListVector* thisList) {
                        string bin = list->get(i); 
                        
                        vector<string> names;
-                       splitAtComma(bin, names);  //parses bin into individual sequence names
+                       m->splitAtComma(bin, names);  //parses bin into individual sequence names
                        
                        //parse bin into list of sequences in each group
                        for (int j = 0; j < names.size(); j++) {