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

[mothur.git] / mergefilecommand.cpp

diff --git a/mergefilecommand.cpp b/mergefilecommand.cpp
index a076281035ff08fdb2ba0af591dce24f726cd636..098da009eaeacfab076c9ad0f800f626158f4a15 100644 (file)
--- a/mergefilecommand.cpp
+++ b/mergefilecommand.cpp
@@ -40,7 +40,7 @@ MergeFileCommand::MergeFileCommand(string option)  {
                        
                        string fileList = validParameter.validFile(parameters, "input", false);                 
                        if(fileList == "not found") { m->mothurOut("you must enter two or more file names"); m->mothurOutEndLine();  abort=true;  }
-                       else{   splitAtDash(fileList, fileNames);       }
+                       else{   m->splitAtDash(fileList, fileNames);    }
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        string outputDir = validParameter.validFile(parameters, "outputdir", false);            if (outputDir == "not found")   {       outputDir = "";         }
@@ -55,19 +55,19 @@ MergeFileCommand::MergeFileCommand(string option)  {
                        else{
                                for(int i=0;i<numInputFiles;i++){
                                        if (inputDir != "") {
-                                               string path = hasPath(fileNames[i]);
+                                               string path = m->hasPath(fileNames[i]);
                                                //if the user has not given a path then, add inputdir. else leave path alone.
                                                if (path == "") {       fileNames[i] = inputDir + fileNames[i];         }
                                        }
                                        
-                                       if(openInputFile(fileNames[i], testFile)){      abort = true;   }
+                                       if(m->openInputFile(fileNames[i], testFile)){   abort = true;   }
                                        testFile.close();
                                }
                        }   
                        
                        outputFileName = validParameter.validFile(parameters, "output", false);                 
                        if (outputFileName == "not found") { m->mothurOut("you must enter an output file name"); m->mothurOutEndLine();  abort=true;  }
-                       else if (outputDir != "") { outputFileName = outputDir + getSimpleName(outputFileName); }
+                       else if (outputDir != "") { outputFileName = outputDir + m->getSimpleName(outputFileName); }
                }
                        
        }
@@ -88,13 +88,13 @@ int MergeFileCommand::execute(){
                if (abort == true) {    return 0;       }
                
                ofstream outputFile;
-               openOutputFile(outputFileName, outputFile);
+               m->openOutputFile(outputFileName, outputFile);
                
                char c;
                for(int i=0;i<numInputFiles;i++){
                        ifstream inputFile; //declaration must be inside for loop of windows throws an error
                        
-                       openInputFile(fileNames[i], inputFile);
+                       m->openInputFile(fileNames[i], inputFile);
                        
                        while(!inputFile.eof()){        
                                if (m->control_pressed) { inputFile.close(); outputFile.close(); remove(outputFileName.c_str()); return 0;  }