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

[mothur.git] / readotucommand.cpp

diff --git a/readotucommand.cpp b/readotucommand.cpp
index 5b9cde8c84b10e0d4f6dd938dbf68191000930f4..efd7073fae39fd493ef28f22d81d6bfdcf795859 100644 (file)
--- a/readotucommand.cpp
+++ b/readotucommand.cpp
@@ -45,7 +45,7 @@ ReadOtuCommand::ReadOtuCommand(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;             }
                                }
@@ -53,7 +53,7 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
                                it = parameters.find("order");
                                //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["order"] = inputDir + it->second;            }
                                }
@@ -61,7 +61,7 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
                                it = parameters.find("shared");
                                //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["shared"] = inputDir + it->second;           }
                                }
@@ -69,7 +69,7 @@ ReadOtuCommand::ReadOtuCommand(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;            }
                                }
@@ -77,7 +77,7 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
                                it = parameters.find("sabund");
                                //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["sabund"] = inputDir + it->second;           }
                                }
@@ -85,7 +85,7 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
                                it = parameters.find("rabund");
                                //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["rabund"] = inputDir + it->second;           }
                                }
@@ -93,7 +93,7 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
                                it = parameters.find("ordergroup");
                                //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["ordergroup"] = inputDir + it->second;               }
                                }
@@ -101,7 +101,7 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
                                it = parameters.find("relabund");
                                //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["relabund"] = inputDir + it->second;         }
                                }
@@ -159,7 +159,7 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = ""; }
                        else { 
-                               splitAtDash(groups, Groups);
+                               m->splitAtDash(groups, Groups);
                                globaldata->Groups = Groups;
                        }
 
@@ -176,7 +176,7 @@ ReadOtuCommand::ReadOtuCommand(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;  }
                                globaldata->labels = labels;
                        }