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

[mothur.git] / readtreecommand.cpp

diff --git a/readtreecommand.cpp b/readtreecommand.cpp
index 07aa5b3e4071289a25400e7cb03f616b34ad18ba..deae495a2171c6af3d117436920558f2e10e7a27 100644 (file)
--- a/readtreecommand.cpp
+++ b/readtreecommand.cpp
@@ -44,7 +44,7 @@ ReadTreeCommand::ReadTreeCommand(string option)  {
                                it = parameters.find("tree");
                                //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["tree"] = inputDir + it->second;             }
                                }
@@ -52,7 +52,7 @@ ReadTreeCommand::ReadTreeCommand(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;            }
                                }
@@ -60,7 +60,7 @@ ReadTreeCommand::ReadTreeCommand(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;             }
                                }
@@ -199,13 +199,13 @@ int ReadTreeCommand::readNamesFile() {
                globaldata->names.clear();
                
                ifstream in;
-               openInputFile(namefile, in);
+               m->openInputFile(namefile, in);
                
                string first, second;
                map<string, string>::iterator itNames;
                
                while(!in.eof()) {
-                       in >> first >> second; gobble(in);
+                       in >> first >> second; m->gobble(in);
                        
                        itNames = globaldata->names.find(first);
                        if (itNames == globaldata->names.end()) {  
@@ -213,7 +213,7 @@ int ReadTreeCommand::readNamesFile() {
                                
                                //we need a list of names in your namefile to use above when removing extra seqs above so we don't remove them
                                vector<string> dupNames;
-                               splitAtComma(second, dupNames);
+                               m->splitAtComma(second, dupNames);
                                
                                for (int i = 0; i < dupNames.size(); i++) {     nameMap[dupNames[i]] = dupNames[i];  }
                        }else {  m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); globaldata->names.clear(); return 1; }