fixes while testing 1.33.0

[mothur.git] / mergefilecommand.cpp

diff --git a/mergefilecommand.cpp b/mergefilecommand.cpp
index cece52d9cd06b78950f5b197c19d2e9574b7daa8..643cf287bb9aded0847390aeea1091c12e95dd74 100644 (file)
--- a/mergefilecommand.cpp
+++ b/mergefilecommand.cpp
@@ -12,10 +12,10 @@
 //**********************************************************************************************************************
 vector<string> MergeFileCommand::setParameters(){      
        try {
-               CommandParameter pinput("input", "String", "", "", "", "", "",false,true); parameters.push_back(pinput);
-               CommandParameter poutput("output", "String", "", "", "", "", "",false,true); parameters.push_back(poutput);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter pinput("input", "String", "", "", "", "", "","",false,true,true); parameters.push_back(pinput);
+               CommandParameter poutput("output", "String", "", "", "", "", "","",false,true,true); parameters.push_back(poutput);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
@@ -41,7 +41,6 @@ string MergeFileCommand::getHelpString(){
                exit(1);
        }
 }
-
 //**********************************************************************************************************************
 MergeFileCommand::MergeFileCommand(){  
        try {
@@ -64,7 +63,7 @@ MergeFileCommand::MergeFileCommand(string option)  {
                if(option == "help") {
                        help();
                        abort = true; calledHelp = true;
-               }
+               }else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                else {
                        vector<string> myArray = setParameters();
                        
@@ -130,32 +129,13 @@ int MergeFileCommand::execute(){
        try {
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
-               ofstream 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
-                       
-                       m->openInputFile(fileNames[i], inputFile);
-                       
-                       while(!inputFile.eof()){        
-                               if (m->control_pressed) { outputTypes.clear(); inputFile.close(); outputFile.close(); remove(outputFileName.c_str()); return 0;  }
-                       
-                               c = inputFile.get(); 
-                               //-1 is eof char
-                               if (int(c) != -1) { outputFile << c; }   
-                       }
-                       
-                       inputFile.close();
-               }
-               
-               outputFile.close();
+               m->mothurRemove(outputFileName);
+               for(int i=0;i<numInputFiles;i++){  m->appendFiles(fileNames[i], outputFileName);  }
                
-               if (m->control_pressed) { outputTypes.clear();  remove(outputFileName.c_str()); return 0;  }
+               if (m->control_pressed) {  m->mothurRemove(outputFileName); return 0;  }
                
                m->mothurOutEndLine();
-               m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+               m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                m->mothurOut(outputFileName); m->mothurOutEndLine();    outputNames.push_back(outputFileName); outputTypes["merge"].push_back(outputFileName);
                m->mothurOutEndLine();