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

[mothur.git] / libshuffcommand.cpp

diff --git a/libshuffcommand.cpp b/libshuffcommand.cpp
index 219b0bf5fcb7149ff20ee7d65563ec1932147bf0..773d8d351211f3ab9794770e72aad77235754b53 100644 (file)
--- a/libshuffcommand.cpp
+++ b/libshuffcommand.cpp
@@ -47,7 +47,7 @@ LibShuffCommand::LibShuffCommand(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->getPhylipFile()); //if user entered a file with a path then preserve it        
+                               outputDir += m->hasPath(globaldata->getPhylipFile()); //if user entered a file with a path then preserve it     
                        }
                        
                        //make sure the user has already run the read.dist command
@@ -61,7 +61,7 @@ LibShuffCommand::LibShuffCommand(string option)  {
                        if (groups == "not found") { groups = ""; savegroups = groups; }
                        else { 
                                savegroups = groups;
-                               splitAtDash(groups, Groups);
+                               m->splitAtDash(groups, Groups);
                                globaldata->Groups = Groups;
                        }
                                
@@ -215,8 +215,8 @@ int LibShuffCommand::printCoverageFile() {
        try {
 
                ofstream outCov;
-               summaryFile = outputDir + getRootName(getSimpleName(globaldata->getPhylipFile())) + "libshuff.coverage";
-               openOutputFile(summaryFile, outCov);
+               summaryFile = outputDir + m->getRootName(m->getSimpleName(globaldata->getPhylipFile())) + "libshuff.coverage";
+               m->openOutputFile(summaryFile, outCov);
                outputNames.push_back(summaryFile);
                outCov.setf(ios::fixed, ios::floatfield); outCov.setf(ios::showpoint);
                //cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);
@@ -311,8 +311,8 @@ int LibShuffCommand::printSummaryFile() {
        try {
 
                ofstream outSum;
-               summaryFile = outputDir + getRootName(getSimpleName(globaldata->getPhylipFile())) + "libshuff.summary";
-               openOutputFile(summaryFile, outSum);
+               summaryFile = outputDir + m->getRootName(m->getSimpleName(globaldata->getPhylipFile())) + "libshuff.summary";
+               m->openOutputFile(summaryFile, outSum);
                outputNames.push_back(summaryFile);
 
                outSum.setf(ios::fixed, ios::floatfield); outSum.setf(ios::showpoint);